


Into the Unknown

by Kyouryokusenshi



Category: The X-Files
Genre: Angst and Hurt/Comfort, Domestic Fox Mulder/Dana Scully, F/M, Post-Episode: s11e10 My Struggle IV, Pregnant Dana Scully, The X-Files Revival
Language: English
Status: Completed
Published: 2018-06-21
Updated: 2018-12-30
Packaged: 2019-05-26 16:38:31
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 36
Words: 41,277
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/15004994
Author URL: https://archiveofourown.org/users/Kyouryokusenshi/pseuds/Kyouryokusenshi
Summary: After discovering Scully is pregnant with their 2nd child, Mulder faces the consequences of his actions against Purlieu and The X-Files are closed for good. What happened to Skinner and Reyes? Is the Smoking Man really dead? Are the threats against humanity really over? What role does William/Jackson play in all of this? This is my attempt to make sense of what CC did not. COMPLETE!





	1. Chapter 1

**Author's Note:**

> Since there were so many questions unanswered and little resolution to the storyline after MSIV, this is my take on Season 12 in which I hope to tie up all the loose ends CC left for us in a more satisfying manner. Some references to Scorpion. I started this story over on Instagram as @iwtb.scully and it currently has over 50 parts and going. Many thanks to Marina Frenzy for being my BETA on this!

They were both overwhelmed with emotion. This wasn't how Scully wanted to tell Mulder about the baby. She never got to tell him properly 18 years ago, so she had wanted it to be perfect this time. He was so heartbroken when she all but told him William wasn't his. How could she not tell him then? Part of her felt awful she was having another child after everything that happened. Could they keep the baby safe? Would she fail her like she failed William? As much as she was afraid something would go wrong, she already loved the tiny being growing inside of her. The thought of losing her was terrifying.  
  
As they stood out in the freezing cold of the dock harbor, Mulder cried with Scully. They heard nothing but the sound of the gusty wind as it blew against them and the sound of angry waves crashing against the pier. They cried for the loss of their son and the newly announced impossibility. It was bittersweet really, they were overwhelmed with both grief, shock, and happiness at the same time. When she placed his hand on her abdomen, the bump was unmistakable. He was really going to be a father. He had so many questions and wasn’t sure where to start.

“How long have you known?” he finally whispered in her ear.

“Only a few days, I was going to tell you when I came over, but—“her voice broke. “I was also afraid, that a child wouldn’t be something you wanted at this point in your life.”

“I do want it,” he said quickly. “Nothing has ever been practical for us, Scully, but I want to be there, for all of it.”

Mulder placed his hand back on Scully's abdomen to make sure this wasn't all a dream. If you didn't know what to look for, it wasn't noticeable. But now that he knew, he wondered how he hadn’t noticed her changing body.

Scully was overwhelmed and pregnancy hormones weren't helping anything. Instead of dealing with menopause like other women her age, she was pregnant. She couldn't bring herself to tell Mulder that William wasn't his. To voice the words. William was still her biological child, but she wanted to soften the blow by telling Mulder they weren't meant to be his parents, to share in his pain and anguish. _‘He was just an experiment, never meant to be’_ , the words had come out all wrong and Mulder's resolve was breaking. So she had told him she was pregnant, hoping it would be enough to give themselves something to hope for.

The pregnancy was still surreal to Scully, despite having blood tests confirmed by the doctor. She had stared at the hCG levels for the longest time. High levels of hCG weren’t just an indicator of pregnancy. It was something she had been afraid of when the three positive pregnancy tests she bought at the drug store stared back at her. Cancer. It had been terrifying at first, but it wouldn’t have explained the weight gain. Then she had received the vision from William shortly before she got the call from her doctor to confirm the results. The one with her baby's ultrasound and herself giving birth. It was an awful time to tell Mulder, but she couldn't hold it back after hearing what he said. She had to admit that she had been wanting to share that moment with Mulder ever since he ran out that door. She was relieved. Scully feared his reaction, but she had so badly wanted to share that moment with him. Once she had the vision of Mulder getting shot, she was terrified that she would lose him before she got to tell him about the baby.

 

Still in his arms, she had stopped crying. The flashlight she was holding dropped to the ground with a clatter, startling them both. Mulder gently pulled back and cupped Scully's chin while he looked her over. They both hadn't slept in well over twenty-four hours. "We should go...you need to rest," he insisted. 

  
Scully opened her mouth to protest and then looked back up at him in startling realization. The gunshots. She had forgotten all about it when William had stopped her. "Skinner," she said.

"Skinner is with you?" Mulder was relieved she didn’t come alone. She had a tendency to go into dangerous situations without back up.  
  
Scully nodded. She had a bad feeling. Skinner should have caught up to them by now. 

  
Mulder nodded. "Okay, let's go." 

\---

Jackson swam to the bottom of the pier. He could hear his birth mother crying in Mulder's arms. One thing was clear. Mulder believed he was his birth father this whole time and he wanted so badly for that to be true. The undying love he saw in the man's eyes was the same love he recognized in his mother. She was going to help her friend outside, but he had to stop her or she would have gotten seriously injured as well. It was his chance to escape, but he needed to make sure both she and the baby she was carrying were safe. Few things remained in this world that he cared about. His birth mother, the man who thought he was his father, Mulder, and the little brother or sister he felt an uncanny attachment to.

He saw the baby in their shared visions that he shared with her. He suspected that she didn't know about it until the past few days, because she had just told Mulder about it. It was one of the reasons she was crying again. He had seen her in his visions from time to time for as long as he could remember. As he tapped into his powers, he began to feel and see her sadness. He wasn’t quite prepared for her revelation in the morgue, however. He could feel the overwhelming guilt she had for giving him away and wanting to see him again. It was difficult for him to wrap his head around. He knew she loved him and hoped the baby would make her smile again. From what he knew of her in his visions alone, she had longed to be a mother and never expected to have the chance again.

Jackson sighed. He the smoking bastard in the water, but just as soon after, the body was gone.

\--

When Mulder and Scully made it back to the alley, they had found Monica Reyes and Walter Skinner. Both were critically injured and needed immediate medical assistance. Scully felt responsible. She was the one who asked for Skinner's help and she didn't go to help him when she heard the gunshots. Later, she cried into Mulder's chest as both of their friends were loaded onto stretchers and into ambulances. "He was helping me, Mulder," her voice broke. "Helping us. I brought him into this, it's all my fault." Mulder wrapped his arms around her protectively.

This amazing woman was giving him a child at such a high risk. He never imagined he could love her any more than he did right then and he would give up everything to protect them both. Mulder felt bad that he had doubted Skinner and it terrified him that it could have been Scully under that car.

"It's not your fault, Scully. None of it is," he soothed. He pulled back slightly and Scully moved to wipe the tears from her face as he placed his hand back on her abdomen to feel the small rounded swell. It was impossible, but the impossible had happened.

 


	2. Chapter 2

Reyes and Skinner were transported to Our Lady of Sorrows hospital. Scully wanted to ensure they got the best care. Mulder and Scully were tired. He knew he needed to get Scully home where she could rest. Her advanced maternal age made her a high-risk patient. On the drive back home, Mulder continued to look over at Scully as she slept. Her expression was pained and her hands curled protectively around her abdomen. Mulder thought about how he wouldn't hesitate to kill anyone who tried to hurt them. Just as he mercilessly killed people at Purlieu and even his own bastard of a father for shooting William. The son he thought was his the past seventeen plus years.

He thought back to when he talked with Scully while on the road. There was a tremor in her voice each time she spoke. " _Just come back alive_ ," she had said. Even when he left the house, it was strange and unlike her to not go with him to find William. Would he have left had he known she was pregnant?

  
When they pulled up on the long graveled driveway, Scully was still fast asleep. He looked to see that his own phone had blown up with messages from Kersh. He hadn't bothered to check it earlier.

"Scully, we're home," he finally whispered. He hated to wake her.

She roused and took in her surroundings once he said the words.

Without a word, she reached for the door handle and let herself out before he could get out of the car.

He hurried to her side, placing his hand on the small of her back as they walked up the footsteps.

"Let's get some sleep and then we can figure everything out."

\---

Scully woke up to the soft morning light that filtered in through the window. It took her a moment to realize she was in the warm, familiar bed she and Mulder had once shared for so many years. She turned to see him fast asleep beside her, on top of the blankets. He had shed his bloodied coat but remained in his long-sleeved shirt and jeans. 

  
Was he so busy making sure she was comfortable that he forgot to care for himself? Mulder generally had bad insomnia.  This morning though, it looked like he had passed out shortly after he brought her to bed. She couldn’t recall their trip home. The baby...William, Skinner, and Monica. William's paternity. It was all too much. She couldn't help it as the tears came flooding back as she remembered the events of last night.

They had suffered so much loss as if they hadn't already lost enough. They had gained something though. She was having a baby and she and Mulder would be a family again. She brought her hands to rest on top of her abdomen, feeling the familiar unmistakable bulge. "Hi baby," she whispered as she caressed the small bulge. It was unreal.

She couldn't help it as the tears came flooding back. She was startled by the voice next to her. "Hey," Mulder whispered. "You okay?" He looked at her worriedly. 

  
Scully turned towards him, releasing a slow breath and forced a nod. He just found out he wasn't a father after seventeen years and witnessed their son getting shot, but he was always concerned for her. "You slept all night like that?" Scully asked.

Mulder shrugged. "I'm used to it. How is the baby?" He asked, moving closer.

Scully took Mulder's hand and guided it to her lower abdomen. "Fine, I think." Scully knew she had overdone it yesterday with all that running. "I can't feel any movement just yet, but I’m nauseated and hungry."

Mulder smiled. "Did you know for very long?"

Scully shook her head. "No, I just found out and honestly, it still doesn't feel real to me. I just thought I was gaining weight.”

Mulder nodded, he was still in awe that there was a tiny life growing inside of Scully. She was supposed to be barren and they were in their 50's. "How far along are you?" He asked.

Scully smiled. They had only been intimate a few times in the last couple of months. "If I had to guess," she said with a smirk, "Thirteen weeks since I'm already showing some. I will find out for sure next week. It’s common to show much sooner the second time around. The uterus doesn't completely return to its original size. Births also tend to be quicker, but then again, that was over seventeen years ago." She watched as Mulder's features started to depress again at the mention of William. "Mulder...I need to tell you something," she insisted.

He nodded at her to continue.

"After last night, nothing else you say will have the same shock value."

Scully smiled and took Mulder's hand into hers. "William is alive," she said.

"Scully..."

  
"No, Mulder. I know he is. I can feel him. He's not gone. Despite my vision, I never believed he was dead." 

Mulder hoped she was right and that if William was still alive, he would come back to them. He didn't care about paternity. William was Scully's child and therefore his child too.

They were startled by the sound of Scully's cell phone downstairs. Scully looked over at Mulder and hopped out of bed before he could say anything further. She rushed down the stairs and recognized the familiar number of her hospital on the phone screen. "Hello?"

"Hi, Doctor Scully?"

"Yes, this is Doctor Scully."

"This is Doctor Joyet, I wanted to let you know that the patients whose transfer you arranged, a Walter Skinner and Monica Reyes are in stable condition."

"Oh, Thank God," Scully breathed a sigh of relief as she paced the living room.

Mulder walked down the stairs behind her, checking his own phone.

"I just thought I'd let you know in case you'd like to see them. Mr. Skinner has a broken leg, fractured pelvis along with a concussion, but he's going to make a full recovery in time with proper rehabilitation. Ms. Reyes had a bullet wound that fractured the skull. It's amazing she survived."

The doctor didn’t need to elaborate that it could have been a clear shot. Scully had seen her fair share of miracles. The one inside of her was a testament to the impossible being possible. "Well, I've seen my share of improbable recoveries, Doctor Joyet. Thank you. I'll be there as soon as I can." Scully hung up the phone and looked over at Mulder. "Skinner and Reyes are going to be fine," she felt the tears coming on. Damn hormones. "It could have been worse."

Mulder nodded. "In not so great news, Kersh is demanding answers for all of this. Including for what happened to Skinner and the sudden reappearance of Reyes. I think he blames me."

"Kersh isn't going to let this go, Scully," he continued.

Scully sighed. "When is he expecting us?" Mulder shook his head. "Right now. But I can go, it's me he wants anyway." Truth was that he didn't want Scully to bear Kersh's wrath or take the blame for his actions. She had been through enough.

"Okay, I need to check on Skinner and Reyes." She moved to grab her keys but was startled as Mulder grabbed onto her.

"Scully, wait." She turned as he pulled her back to him. He cupped her face and kissed her deeply, the intimacy bringing a familiar sense of comfort amidst all the chaos and darkness in their lives. They savored the moment for a minute before Mulder pulled back. He stroked her cheek gently with his thumb."I love you both."

Scully's eyes began to water. He hadn't kissed her quite like that since they had separated. Now wasn't the time for hormones. She had to get going before she lost it. "I know, I love you too." 

 

To be continued...


	3. Chapter 3

Scully knew it would take her about 45 minutes to get to the hospital from their house, after all, this had been her daily commute for so many years. Once she arrived, she asked for the rooms of Walter Skinner and Monica Reyes and reviewed their medical charts. Thankfully, their rooms weren't too far away from one another. Reyes was due to be released soon. She had a mild concussion and a grazed bullet wound which had been bandaged. If any further to the left and her injury would have been fatal. Monica was lucky to be alive. Scully stopped outside of Skinner's room. A wave of guilt hit her. She took a deep breath and went inside. Skinner's leg had been cast and was raised. His head was also bandaged. There were some cuts and bruises on his face. the paperwork indicated he had also had a fractured pelvis as, but thankfully there was no internal bleeding. Still, rehabilitation therapy would be in order. 

  
Skinner managed to turn his head upon hearing her footsteps.

"Dana," Skinner said. Relief was evident in his voice.  
  
Scully moved closer to him, looking over his injuries quickly. "Sir...I..I'm so, so sorry," her voice wavered. "This happened to you because of me." She touched the top of his hand.  
  
Skinner shook his head. "Agent Scully, no. It's not your fault. I chose to come with you, just as I said I've always chosen to have yours and Mulder's back, remember?"

Scully couldn't say anything. She felt horrible about what happened. She should have been there, she might have been able to interfere, to make a difference, but Mulder...no, William, had stopped her.

"Did you find him?" Skinner finally asked.  
  
Scully looked away for a moment, contemplating before turning back to him.

"He was shot, by that black lunged asshole. By the time Mulder and I caught up to him..." her voice broke at the too fresh memory.

Skinner opened his mouth in horror as he watched Scully's face contort in pain. If he wasn't stuck to this bed, he'd hug her.

"Oh God...Dana, I had no idea. I can't imagine...I'm so sorry," he said feeling guilt settle over him.

  
Scully shook her head suddenly. "I can't really explain it, but I think he is alive. I don't want to get into it here, but we have this connection and I think he's alive. I can feel it."

Skinner's eyes went wide in confusion, but he decided not to press the subject. He had no idea what she was talking about, but he had seen enough of the unexplainable to know not to question it.

He narrowed his eyes. "He tried to kill me, Scully. The smoking man. I tried to stop him. He was with Monica."

Scully touched her abdomen absently. "Monica was trying to help us," she said.

"I know it looked like she was working with the smoking bastard, but she was trying to keep us safe. She was trying to help us." Scully recalled her meeting with Monica in her vision and she was anxious to talk to her friend. "She's alive, miraculously," she said.

"I shot her..." Skinner replied. 

  
She touched his shoulder. "Don't blame yourself, Sir."

Skinner almost laughed. "I'm pretty sure you won't be calling me that much longer. If I'm not already out of the bureau, I'm retiring. I'm done."

Scully went to see Reyes next. The door of the room was ajar and she saw Monica getting ready. The brunette was startled by her presence and looked up from putting on her shoes. Aside from long, curled hair, Monica Reyes had barely aged a day since Scully had seen her sixteen years ago. The taller woman was surprised by her appearance and rushed towards her, pulling her into a tight embrace.

"Oh my God, Dana! You're okay," she teared up.

Scully couldn't hold back the tears either as she wrapped her arms around her friend. She didn't really have any other close female friends. Monica pulled back a moment later and it was then that Scully took note of the bandage on her head.

"I'm sorry, Dana. For everything that's happened. I tried to stop him. I wanted you to find William. You have to believe that I'd never betray you or Mulder."

Scully looked up at her through tears. "I know, I know you did. He tried to get Skinner too."

"And I was an unwitting participant in that and I paid for it when he shot me," Monica laughed nervously.  
  
Scully knew that Skinner was always on a tight rein with the smoking man. There were also Marita and Krycek. That black lunged sonofabitch always needed a pawn in his sick game.

"What is it, Monica?" She asked. "He's gone now," Scully insisted. 

  
Monica swallowed and Scully knew her friend was holding something back.

"I don't think he can be killed," said Monica.

It was one of Scully's worst fears, but what Monica was saying made sense. The bastard had survived a missile strike.  
  
She sighed. Another question had been on her mind. "Where is Agent Doggett? I tried to look both of you up when I came back to the FBI," said Scully.

Monica lowered her head, sitting back on the hospital bed. Having worked with the smoking man enabled her to have access to just about any type of data she needed.

"John is working deep undercover in Homeland Security under another name," she whispered. 

John was often in her thoughts over the past decade. She knew where he was and what he was up to. Being a double agent undercover had its benefits. The guilt of leaving him suddenly without any explanation never escaped her.

Once Monica was discharged, she went with Scully to Skinner's hospital room. Skinner looked up at them both in shock. "Agent Reyes...Monica?"

Monica smiled. "You haven't killed me yet, sir."

Both Skinner and Scully stared at her in shock and her grin quickly faded.

"Sorry, bad joke. Too soon?" asked Monica.

"I'm sorry Agent Reyes, I thought..."

"I tried to stop him, Skinner. He grabbed the wheel when I tried to get out of there.”

Skinner nodded. "I know."

An uncomfortable silence filled the room. Scully moved to close the door before she decided to speak.

"I wanted Mulder to be here for this, but since Monica is leaving tonight, I feel it is only appropriate that I share this with the both of you now."

Both Skinner and Reyes looked at her in confusion.

"It might sound a little absurd and I know it is impossible, but the truth is, I am expecting."

\---

Mulder felt like a guilty kid called to the principal's office when Kersh's secretary told him he could go in. He knew what was coming. It didn’t matter, he planned to retire from the FBI and build a life with Scully and their baby and maybe Jackson, too. He hadn't realized how much he had wanted that until fatherhood was taken away from him.

"Agent Mulder," came Kersh's terse tone of voice. "Have a seat," he instructed, pointing to the chair in front of him.

"I prefer to stand, Sir."

Kersh sighed with resignation. "I assume you know why you're here, Agent Mulder?"

"Let's just cut the crap and get to the part where I hand you my badge and gun."

"An assistant director and federal agent were in serious condition as a result of this silly charade of yours," said Kersh.

Mulder didn’t reply. It was true.

"Add that to the outrageous statements you made on Tad O' Malley's site. Statements about the unleash of some plague that would wipe out humanity."

Mulder recalled Scully going to Tad O' Malley to leak that information hoping it would go viral. He wasn't going to tell Kersh that though. Scully still had a chance to go back to her career as a medical doctor and he wasn't about to put that stress on her or the baby. It was something everyone expected of Spooky Mulder, which is why he gave her permission to use his name.

"Mmm hmm."

"Oh and I also got a call from Purlieu...said that you made an unannounced visit."

Now that got Mulder's attention. His blood went cold. Kersh didn't say anything further, however.

"It's over, Agent Mulder. Your career with the FBI and your ridiculous quest for this...'truth'."

Mulder just about rolled his eyes and began to pull out his badge and gun as Kersh continued.

"You and Agent Scully are both done. The X-Files is done. A.D. Skinner will face mandatory retirement and you can bet your ass you won't walk the halls of this building ever again," said Kersh. 

Mulder threw him a slight nod, then walked out determined never to look back.

To be continued...


	4. Chapter 4

**Notes for the Chapter:**

> I'm back from L.A. and my wonderful beta sent me another chapter to post :)

The room was uncomfortably silent at Scully's revelation. Monica and Walter didn’t move, they just watched in shock as Scully struggled to hold back tears. Part of her still couldn't believe the news. After taking another deep breath, she finally spoke up, "I know it's impossible. It's a miracle. I always feared the truth about William’s conception from the moment I found out I was pregnant. But this time things are different. I know with absolute certainty that this child wasn't part of any experiment." Scully thought back to the vision of the ultrasound William shared with her. Thirteen weeks. There was only one possible night she could have conceived. One thing she couldn't explain, however, was how she knew this baby was a girl. Maybe that was just maternal instinct.  
  
Skinner thought back to the car ride over to Norfolk and felt terrible. He sensed something was up when Scully asked for his help, but back then he didn't think too much of it. She had come to him before when Mulder had taken that case with Father Joe into his own hands. He wasn't sure he would have told Scully about William had he known she was carrying another child. He couldn't even begin to imagine how that knowledge might have affected her current pregnancy. "I assume Mulder knows?" he asked.

Scully nodded.

"Congratulations, Dana. I mean it," Monica said.

"Thank you."

Monica pulled her friend in for a tight hug. She would have known before anyone else if the smoking bastard had laid another hand on her. This was a miracle. "You're right, Dana," Monica said as if to assuage any fears her friend might be holding back.

"It is a miracle. If there was any....intervention, I would have told you,” said Monica.

Scully smiled and nodded. She had planned to keep the baby a secret for a little while longer, but she didn't know when she'd see her friend again. It was comforting to be able to share this knowledge with a trusted friend, especially since she delivered her first child.  
  
Just then, the door to Skinner's room was thrown open.

Scully and Reyes startled and turned around to be met face to face with Kersh. To say he looked pissed off was an understatement. "Step outside Agents," he ordered. 

Scully narrowed her eyes before turning back to Skinner who nodded as if to tell her to go along with it.  
  
Monica looked over at Scully as they both left the room.

"What is going on here?" Scully demanded.

"What's going on is that an Assistant Director was nearly killed because of your and Mulder's crusade," Kersh spat before turning to Monica, "and another FBI Agent injured."

"Sir," Monica started, "that's not--"

Kersh held his hand up. "You're free to go, Agent Reyes," he said in a tone that indicated he was finished.  
  
Monica turned towards Scully and concurred. They had exchanged contact information earlier and had agreed to get in touch once she met up with John.  
  
Scully managed a small smile as her friend turned and walked away.  
  
Kersh watched the brunette leave before turning back to Scully. "Now I already told Agent Mulder. The X-Files are closed. Even though he is responsible for this, I don't doubt for a minute you were involved in some way. Calls were placed by you from his residence. Not just recently, but on several occasions. Including the incident with Purlieu services."

Scully opened her mouth to speak but couldn't find the words.

"On top of that, I found something else. A marriage certificate indicating you and Mulder got married in the state of Virginia back in 2002. I don't know how on earth that was overlooked when you returned to the bureau, but the Assistant Director will be facing his own disciplinary action for assisting you both with this ridiculous quest."

Scully began to feel the rage boiling through her veins. She knew where Kersh was going with his accusations. She reached into her coat and thrust her gun and badge at him. "You may be able to keep me from walking the halls of the FBI. But this is MY hospital, you can't keep me from making sure he gets the care he needs," she said icily.

Scully quickly brushed past Kersh. Her emotions were bubbling to the surface. The events of the past 48 hours were catching up to her again. 

As she made her way down the corridor to the front entrance of the hospital, she saw Mulder coming towards her, worry evident in his features.

"Scully," he said, relieved to see her. When he saw her face, he knew something was wrong. She said nothing but allowed him to place his arms around her shoulders.

Together, they left the hospital. When they arrived at Mulder’s car, Scully checked to see if they were alone, then pulled Mulder close and sighed as he wrapped his arms around her. She liked to maintain a strong public demeanor, but today she allowed herself to crumble in Mulder's arms. His embrace was a great comfort. He was the only person aside from her mother who had seen her true self, including her vulnerable side.  
  
They knew the X-Files would be closed because of everything that happened. Their son was the reason they came back to the bureau in the first place. Finding him so they could stop the virus was the only thing that mattered. What was left to search for now? They found their son but had to let him go. They had to focus on their new baby.

Mulder and Scully returned home a short while later. She told Mulder that she had a chance to see Monica Reyes before she was discharged and that she would stay in touch with her after she located John Doggett in California. "Kersh knows about the marriage certificate," Scully sighed.  
  
Mulder shrugged. He wasn't entirely surprised. Skinner had pulled a lot of strings to get them back into the bureau. Things were overlooked during that process, including his depression. Technically he shouldn't have even been carrying a gun.  
  
Mulder was still slightly on edge, he knew there were cameras in the Purlieu building. It would only be a matter of time until he would likely face murder charges. He didn't want to scare Scully though. It was the last thing she needed right now. "We did what needed to be done, Scully. Unless you don't want to be married to me anymore," he teased, trying to lighten the mood. 

Even though they had been physically separated for a few years, neither of them had the resolve to file for a dissolution of marriage. They had arrived at the decision to get married following Mulder's trial back in 2002 while they were on the run. It would protect Scully from ever having to testify against him again, should it ever come to that. A piece of paper didn't dictate their feelings, however. The feelings they had for one another were more complex and went beyond the widely understood definition of marriage. 

Scully smiled. "Of course, I do, and I don't want to hide it anymore. We're having a child together, Mulder. I want us to be a family officially. But no one is going to call me Mrs. Fox Mulder."

"Understood," he said as he wrapped his arms around her. "No more telling people I'm not your husband though. We both know that's a lie."

"We should probably get rings, huh?" Mulder smiled. The idea of living together officially as a married couple with their baby filled him with overwhelming happiness. 

Scully smiled. "Yeah, but it has to be something fairly practical. We can't always wear rings at the hospital."

They hadn't really discussed where they would go with the X-Files being closed, but Mulder imagined Scully would eventually go back to work at the hospital. "Okay, we can plan a trip to Kay Jewelers after our trip to IKEA."

"I thought we already made all those repairs after the incident with Purlieu," Scully said.

The mere mention of that name made Mulder's blood run cold again. He pushed that thought from his mind. "Well, we should probably start getting ready for the baby. You're already more than three months along, we have less than six months to get everything ready!" Mulder reached out and touched the small rounded bump of her abdomen. 

Scully smiled and placed her hand over his. "Oh...you're right. I still can't believe this is happening."

The sound of tires hitting the graveled driveway startled them both and Scully moved towards the kitchen window. "Were you expecting someone?"

Mulder followed closely behind her. "No," he said as a sense of dread settled over him.

Scully pulled back the curtain to see two familiar black SUV's driving up to the front of their house. To her surprise, Mulder pulled her back from the window and placed his hands on her shoulders. Scully was startled by the sudden movement. "Is there something you aren't telling me?" She nearly demanded.  
  
Mulder looked away and sighed, overwhelmed with guilt. 

Scully narrowed her eyes. "Mulder, you're scaring me. Why are they here?" Mulder was terrified, for himself, for Scully, and their unborn child. If he had known she was pregnant, maybe he wouldn't have been so stupid and reckless, but he was using whatever means necessary to get to William.

"Do you remember when I told you William wasn't on the plane when I made that trip to Purlieu services?"

Scully looked at him questioningly and opened her mouth to say something, but couldn't speak as she tried to process what he was saying.

"There may have been a few casualties that involved Mr. Y and others along the way and it wasn't just self-defense."

Scully shook her head and he suddenly saw the fear register in her own eyes at the implications. "What are you saying, Mulder?"


	5. Chapter 5

"They're here for me," he said.

Scully stared at him in overwhelming shock as she registered the meaning of his words.

"No," she exclaimed, shaking her head violently.

They could hear demanding voices over an intercom telling Mulder to come out. Scully began to hyperventilate, her head was spinning. Mulder pulled her into his chest and wrapped his arms tightly around her. If he didn't go, they would take him by force, and he didn't want to risk anything that might hurt Scully. After their last encounter, he knew what these people were capable of.  
  
Scully looked up at him, her eyes full of tears. "No, Mulder. I *need* you," she said, her voice shaking.

"I can't do this alone, not again."

The voices outside were growing impatient. 

Mulder moved his hands to cup her face and pressed his lips to her forehead. "You won't lose me. I will find a way, I promise." Scully blinked and allowed the tears to fall. "Please, go upstairs. Trust me," he said.

Scully hesitated, she didn’t want to let Mulder out of her sight.

They could hear vehicle doors closing. Quickly, Mulder placed his hand over her abdomen and ran his hand over the area where the baby rested. "I love you both so much. Now go, please."

Scully shook her head in fierce determination.

"Scully please, I have to. It's only a matter of time." She took his hand and squeezed it. "I'll find a way to get you out of this. I promise."

It took every ounce of willpower Scully had left to hurry for the stairs. She heard the door open and loud voices yelling Mulder's name and demanding him to exit their home. Shaking, she made her way to the closest window on the second level, careful to remain unnoticed.

It only took seeing Mulder being grabbed roughly and thrown against one of the cars for Scully to break down. She sank to the floor, wrapping her arms around her midsection, and began to sob violently. Just when she thought they couldn't have possibly lost anything else. They lost the X-Files and their son. Skinner and Reyes both nearly died. "Please, not him too," she pleaded and hoped whatever God was out there was listening. "I can't lose him."

Truth be told, without FBI resources, without the help of Skinner, with Doggett and now Reyes in California somewhere, who could she trust? Even if she ran out there, it would have been futile. She also no longer had herself to think about.

\---

Jackson pulled up to the entrance of a property in Farrs Corner, VA. He parked further up the street to remain inconspicuous. When he walked towards the entrance, several black vehicles came speeding out at full speed. He jumped into one of the nearby bushes and hid until he was sure they had all passed by. He gingerly stepped out, plucking the few thorns that stuck to his clothes.

He had tried to ignore the voice in his head that told him to stay far away from Dana and Mulder, but he couldn't help it. His last vision told him something terribly wrong would happen to Mulder. The man had killed several people to get to him, he owed it to them to help him. He could hear devastating sobs coming from his birth mother as he walked towards the single property at the end of the vast driveway. He sensed her fear, not just for Mulder, but also for the baby she was carrying.

\--

Scully wasn't sure how long she was on the floor, but she felt her legs growing numb. She felt guilty for not going with Mulder. The commotion outside had made her lose it and she couldn't bear to watch. She just prayed to whatever God was listening that Mulder was okay. She needed to help him but wasn't sure where to start.

A tiny flutter in her abdomen grabbed her attention. It startled her at first, but then she recognized the feeling even after all these years. The baby had moved. 

She knew it wasn't uncommon to feel the baby move between thirteen and sixteen weeks by the second pregnancy. The first one had been so long ago, but the uterus never fully returns to its normal size. This was why she began to show already, though you could easily miss it if you didn't know what to look for.

She felt more tears building up as she placed her hand on her belly, rubbing at the spot. Everything was surreal. She still expected to wake up one morning and find out this had all just been a dream. She shifted and eased off the floor before her legs started to tingle from lack of circulation.

The baby’s movement caused about of nausea to hit her and she stumbled towards the bathroom in an effort not to vomit onto the floor. She threw the toilet seat up and began to empty her stomach contents. She took several deep breaths until she felt the nausea pass and closed the toilet lid before flushing. Scully folded her arms on top and rested her head there for a moment. Her skin was damp and clammy from the effort.

A moment later, she stood and went to the sink to wash her hands. She stopped and looked back at her reflection as she often did when suddenly her head started hurting a series of images swam in front of her eyes. Mulder in a jail cell, Mulder getting sick, Mulder getting a lethal injection. She groaned and grasped onto the sink to steady herself. Before she had the chance to make sense of what she saw, she was startled by more noise outside.

Scully ran to the bedroom and pulled open the left bed stand drawer. She retrieved her gun from its holster before going back to the window and peering outside. Nothing. Her heart sank slightly at the thought that Mulder was really gone. She sighed and went downstairs and that was when she heard the shuffling movement again. 

Scully opened the living room closet and sure enough, she found a flashlight. Once she retrieved her coat, she slipped it on and walked towards the door. Slowly, she opened it and peered outside, the sun had set some time earlier and she couldn't see much other than what the porch light illuminated. 

The floorboards of the deck creaked underneath her boots as she walked down the steps and around the side of the house. Keeping her right hand tight on her gun, she switched on the flashlight in her left hand. That was when she saw movement in one of the shrubs. Instinctively, she held her gun out in front of her. She certainly didn't expect what she saw next. A tall teenage boy suddenly emerged from the brushes. Scully gasped in shock. "Will--Jackson?!"

 


	6. Chapter 6

**Notes for the Chapter:**

> I hope you guys are enjoying this fic! Please do let me know what you think so far! :)

Scully stared at the young man in front of her in shock. She lowered her gun, but still stood there as if she were planted in place. She wanted to run to him, but she was afraid he would try and run from her again. The teen would undoubtedly outrun her again, especially in her current condition.

Finally, they were face to face with no disguises, but the words just wouldn’t come out of her mouth. Thankfully, he made the first move. "I'm sorry that I ran from you before," he said, taking a step closer. "But both of you were being followed at the time." Jackson didn't want to admit that he was also a little bit scared to finally meet his birth mother. He did his research and he knew she was a medical doctor and now a former FBI agent. He felt she might not approve of him and after he heard what she said on the dock, he was almost certain she regretted finding him.  
  
Scully managed a small teary smile. "It's okay....you're here now." Jackson recently discovered that he had the ability to hear thoughts. It was something he was still learning to tap into and control. Most recently, he was working on filtering out random thoughts, and to his surprise, he was getting a pretty good handle on the process. "My name is Dana," she said. "But I'm sure you probably know that already," she laughed nervously.  
  
He nodded, taking another step in her direction. She wished Mulder were here too, her pillar of strength. "Uh, Mulder...he's in a lot of trouble, isn't he?" asked Jackson. Scully nodded. She was having a hard time holding back tears. The events of the past 72 hours along with the pregnancy hormones were getting to her.

Jackson had always been somewhat awkward. He was embarrassed when his adoptive parents would display affection towards him, and like a typical teenager, he always complained. What he wouldn't give to hug them now. Dana seemed to be the next best thing though and she looked like she could use a hug, so he closed the distance between them and wrapped her in his arms. 

He knew she was in shock, but he felt her embrace him tightly. Her grip was so tight that he could barely breathe. She was small. He was close to a foot taller than her, but she sure was strong. 

  
Scully fought to keep back the tears until she couldn't any longer. But when she felt Jackson's chin on her head, she had to laugh at the similarities. He was Mulder’s son. That black lunged sonofabitch was a liar. She had run all the tests in the world when he was baby. Science wasn't wrong. DNA tests don't lie.

She was crying and Jackson wasn't sure what to do. The last time someone hugged him was when he saw Sarah at her house, but as expected she never showed up at the sugar factory. It felt nice though, to feel loved. It reminded him for a moment of his other mom and dad.

Scully pulled back. "I'm sorry," she said as she brushed away her tears. "Did you want to come inside? We don't have much, Mulder doesn't really go shopping, but I can put something together for us." Jackson was unsure. He swallowed, then eventually agreed to join Scully inside. There was an unmistakable look of relief on her face and a smile. He didn't see her smile much, but he was glad he was the reason for it after feeling like an outcast and burden for so long.

Jackson sat at the table while Scully put some sandwiches together. As he looked around the house, he noticed tons of newspaper clippings in the living room next to a desk. He couldn't help but notice the single photo amongst them. It was of a young girl. He made a mental note to ask them about it later. On the stairs were several rows of randomly stacked books. Random.

"What would you like to drink?"

The sound of Dana's voice startled him back to reality. "Oh umm, I don't suppose you have soda," he laughed. He was surprised to see her smile again.

"Well your fa---Mulder usually keeps some, but I kind of made him get rid of it."

Jackson smiled. He wasn't sure why, but he had totally imagined her to be the type to go on about how unhealthy it was, sugary and all. Maybe it was because he knew she was a doctor. His adoptive mom was the same way and only allowed it on special occasions. "Juice then, please. I'm not picky." Scully moved to go back to the fridge and that was when he realized he had forgotten his manners while being on the run. "Did you, uh, need help with anything?"

She shook her head. "No, thanks."

They sat to eat together at the dining table. Though Scully and Mulder sometimes ate there together, it was surreal having Jackson there. It was quiet for a while before she spoke. "I'm so glad you're okay."

Jackson knew she meant it, he could sense her thoughts. He couldn't exactly read minds, but he was highly perceptive of the feelings and intentions of others as a result of his powers

"Mulder...he saw you get shot. He was devastated. I could sense you were alive though."

Jackson nodded, looking down at his sandwich. "I'm sorry. I'm trying not to send you the visions. I know it's painful."

Though Jackson had become somewhat of a delinquent, he didn't want to harm the ones he loved. What he did to Bri and Sarah he quickly realized was a horrible mistake. If he hadn't done it, maybe his parents would still be alive. He frowned. Dana seemed to sense his melancholy. She reached across the table and placed her hand on his. Maybe it was a mother's intuition this time. To both of their surprise, he didn't pull back.

"Don't worry. It's not your fault. None of this is."

He smiled slightly. But there was something unpleasant he wanted to ask. Something that had been on his mind. "But you said I was an experiment, that I wasn't meant to be."

Scully jerked her hand back as if she just had her finger in an electrical socket. It took her a moment to speak. "I never meant any of those things. I was in shock at the time. I'm sorry. I'm so sorry." He could see she was about to cry again, genuinely disturbed by the words she had uttered on the pier.

Scully sniffled slightly and looked back at her son. There was a small scar on his forehead. "You saved Mulder. He saw you taking on his form that night."

Jackson nodded. "Dana… I shared my vision with you. We both saw a possible future, a terrifying one. When I took his shape, it was because Mulder was going to die. There is a possibility he still might. He's in this situation because of me and I came to help." 


	7. Chapter 7

It warmed her heart that her son wanted to help Mulder. Their shared visions and Skinner's revelation had cast doubt over her mind. She said unthinkable things on that dock, things she wished with all her heart that she could take back. As his mother, she worried for his safety even though she had no doubt he was capable of protecting himself, his powers were dangerous, yet also offered him protection.

"I just need to destroy the surveillance tapes and get inside the heads of those who want to hurt him. I can make it look as if nothing ever happened," said Jackson.

Scully opened her mouth to protest, but she didn't speak. She really had no other way to help Mulder. No resources other than maybe Reyes and possibly Doggett. There was no way they could survive being on the run again, that’s assuming they were able to miraculously get him out in the first place. Not in her current condition. All she wanted was to have her family together and happy. Scully looked at Jackson and nodded reluctantly. She felt the tiny flutter in her abdomen return and unconsciously put her hand there. 'It'll be okay, my little one', she thought. 

  
Jackson watched as his birth mother seemed to get lost in thought. He tried his best to stay out of people's thoughts, but he knew she was thinking about the baby. The baby had moved. When he first sensed the tiny life inside of her, it was very small, faint. Now he heard the sound of a beating heart, strong and loud.

The beginning of new life mesmerized him. He thought back briefly to when he showed his friends how he hatched a chick from a store-bought egg, he had been trying to show off during a science project presentation. Some people thought he was cool, but at the same time it earned him a reputation that made a lot of his classmates afraid of him.

Dana already felt so attached to the baby and he wondered if she shared a bond like that with him while she was pregnant Jackson sensed her anxiety too. Not only because of Mulder's situation but because she worried about whether the baby was okay.

"She's fine," he said without thinking, wanting to reassure Scully. This startled Scully from her thoughts. She gave him a confused look. "The baby," he clarified. Dana looked back at him in shock, not quite sure how to respond.

After a moment, she laughed nervously. "Oh, I keep forgetting you can do that," she said as she recalled the vision he shared with her of the baby ultrasound and her giving birth.

Jackson could tell she felt somewhat relieved as she stood up to clear their dishes. "So you know it's a girl?" She asked, even though she already had a feeling. As she turned to the sink, a smile crept into her features as she imagined telling Mulder they were having a daughter. When she had William, she never thought a second miracle would be possible, but she’d wished she could have given him a sibling. The timing had never been ideal to even try. There was constant chaos and guilt regarding William's adoption. But when Mulder had brought up the possibility of another child back in that hotel room, she thought it would have been nice to have a daughter. A little sister for William. Those thoughts often led to the little girl she never got to know. Emily. The violation she felt at the knowledge of her ova being harvested to create this girl after not long before finding out she couldn't have children. The hope of finally being able to have a child was quickly shattered by her death. She had been seriously ill and had to make the devastating decision to let her go.

"Who is Emily?" Jackson asked suddenly.

Scully turned back to her son in surprise.

"Sorry," he said quickly. "I didn't mean to..."

Scully managed a small smile. "No, it's okay. Emily is...was my daughter. You had an older sister, but she was very sick and she..." Her voice was thick with emotion. 

An older sister. He had always wondered what it was like to have a sibling. He was curious about the baby, but he was afraid he would put her in danger should he stick around. Dana had lost her words. She was shaken. Even though she hadn't said much else, Jackson knew Emily was a lot like him from want he gathered from her thoughts. An experiment of sorts. His mother’s thoughts and his own research into project crossroads told him so. 

  
Scully was growing tired. Not just because of the pregnancy, the day's events had been tiring. "Let me show you the guest room," she said, afraid to hope. To her relief, Jackson nodded and followed her. "You and Mulder should be about the same size. I'm sure I can find you some clothes, though he has bulked up a lot recently." From what he could see, there were three rooms. As they passed by, he assumed the smaller one was for the baby. 

  
The guest bedroom had a small air mattress. "I'm sorry, I know it isn't much. Let me get you some clothes and towels. I'm sure you'd like to shower and change," she managed a small smile.

"Thank you...Dana," he said hesitantly.  
  
It was weird hearing him called her that. It was strange hearing that name in general since her mom passed. Everyone called her Scully. Scully, Doctor Scully, Agent Scully. "Of course," She replied,

Scully went into the bedroom and went through Mulder's drawers to find something for Jackson. As she pulled out his clothes, she stopped and breathed in Mulder's familiar scent. It was familiar, comforting. She thought back to an earlier time when she sought his comfort the first time she was pregnant. It had been just before finding out he had been taken from her.

There was so much Scully wanted to ask Jackson and there was also a lot he wanted to ask her. But they were tired and weary. Scully made sure he was comfortable and told him to help himself to anything he wanted. Jackson said he could help get Mulder of this situation, but at what cost? She felt as if she shouldn't condone this, but the truth was that she needed Mulder now more than ever.

  
Scully decided to don one of Mulder's shirts. The waistbands of her pajamas were growing uncomfortable around her waist. Once she changed, she stopped and stole a glance at herself in the full-length mirror. She pressed her hand to her stomach, still in awe at the tiny life growing in her womb. They had wanted to be parents so badly and they were finally getting another chance.  
  
She turned off the light and slipped under the covers. Normally, she slept on the right side of the bed, but tonight she moved to the middle and breathed in Mulder's scent. She placed her hand over her abdomen and gently stroked the small swell. "Everything is going to be okay," she whispered. Closing her eyes, she prayed that Jackson would still be there by morning.  
  
Jackson changed and got under the covers. He missed having his phone to play around with, but he had to get rid of his last one months ago to avoid being tracked. He started up at the ceiling for a bit before looking around the room and admiring the shelves and decorations. That was when he spotted it, the small familiar windmill snow globe rested on the shelf along with a few other trinkets. He stood up from the bed and walked over, pulling the familiar object into his hands, looking it over carefully. It had been fixed. The plastic was replaced, and the snow refilled. He smiled at the memory. His first impression of Dana had been a fond one.

She was slightly clumsy and distracted due to her grief, but she was very kind. He recalled her friendly smile that she had offered up to him as a total stranger at the gas station while they made casual conversation. And before when he purposely ran into her outside the hospital, simply for an easy excuse to talk to her and she offered up a quick apology when really it should have been him apologizing. He had asked her if she liked snow globes she remarked how she liked that particular one. Those eyes and smile had the ability to illuminate the darkness with the power of a thousand suns. Then he recalled the morgue and her tearful, heartfelt confessions. She loved him so much that she had stolen the snow globe from his room so that she would have something to remember him by.


	8. Chapter 8

**Notes for the Chapter:**

> A little bit of Reyes/Doggett since I think they both deserved better...especially Reyes.

Mulder had been in a place like this sixteen years ago. Cold and dark. The treatment was the same. His feelings were the same, he felt heartbroken and alone. Back then he had learned that Scully had given their son up for adoption. Sitting in a prison cell, he stayed strong for her all those years ago. 

  
It was slightly different this time, however. Kersh, Doggett, and Reyes weren't there to help bail him out. He would be lucky if he got out at all this time. Scully was pregnant and he was terrified that he would lose them. He had been given a second chance and he already screwed up. 

  
Today he was in another prison cell that was cold and dark. His thoughts wandered to her and the baby. Was she okay? Was the baby okay? He wanted nothing more than to be with them. His thoughts then drifted to William. Scully had said she knew he was alive. He hoped and prayed it was true and that they would see him again.

\----

John Doggett was getting ready for bed when he heard a knock on the door. He grumbled as he made his way towards the front of the house. The recipient behind that door was in for an earful, daring to disrupt him late at night. He fetched his revolver from the coffee table and tucked it in the back of his sweats.  
  
Monica took several deep breaths as she replayed, in her head, the words she wanted to say to John after all these years. There was nothing she regretted more than walking out on the love of her life for a life of isolation with the cancer man. 

  
When the door opened, however, that carefully planned dialogue went right out the door. John was slightly heavier than she remembered but still handsome. Aging was marked in the slight receding of his hairline and graying hair, otherwise, this was her John Doggett and he still looked amazing for a 59-year-old man. 

  
John stared back at her in shock. Never in a million years did he expect her to be the person behind that peephole. She was beautiful. Her hair was much longer and she was slightly thinner than he remembered. She had a bandage on her forehead. What happened?

  
Monica's eyes teared up as she smiled back at him. After several moments, she laughed, finally breaking the silence and threw her arms around his neck. "Oh John...John," she repeated. 

John was startled. She had walked out on him that day and he gave up after a few years of no contact. It was as if she had disappeared off the face of the earth. Why now? Despite his confusion, it felt amazing feeling her body against him and he slowly wrapped his arms around her, holding her close.

They stood there for what seemed like an eternity. Monica finally pulled back, wiping away her tears. "Well, you going to invite me in?"

John laughed. She certainly hadn't lost her sense of humor. "Of course, come in. It's cold out here."

"You've been away from D.C. that long?" Monica teased.

"It's balmy here."

"That's SoCal for you. Living the life."

An awkward silence passed between them. Neither was sure where to begin.   
John had so many questions. He watched as Monica took a seat on the couch and set her minimal belongings off to the side. "Can I get you anything?" He offered.  
  
Monica shook her head. "I grabbed a bite after the airport. So you're working for the Department of Homeland Security now?"

John nodded. "How did you find me?" He asked.

"You'd be surprised how many resources a double agent has, John. Or should I call you Cabe Gallo now?"

John smiled. "A double agent huh? So we've both been undercover." Monica managed a smile.

"Something like that. Though I can guarantee you my assignment wasn't so enjoyable."

"So tell me about it," he said.

"It's a long story. I don't know where to start." John moved to sit next to her and placed his hand over hers.

"I have time."

Monica looked at him hesitantly. She hoped what she had to say wouldn't make him send her packing. She decided to start with the easier stuff. "So I saw Dana and Mulder again."

**Notes for the Chapter:**

> Hope you guys enjoyed the Scorpion reference for those of you who are fans. ;)


	9. Chapter 9

**Summary for the Chapter:**

> Lots of fluff and angst ahead! I hope you enjoy this one!

Images of Mulder being beaten in a jail cell startled Scully awake. As she opened her eyes and adjusted to the darkness of the room, she fell back to the mattress and took several deep breaths before her hands came to rest on her abdomen. She felt the tiny, yet distinct movement again as if the tiny life inside was trying to reassure her. She was getting close to fourteen weeks, and she was bigger than she was in her first pregnancy. A few days ago, she decided to download one of those apps that tells you how big the baby is in sizes of various fruits and veggies. This week, the baby was close to the size of a lemon, thinking about it made her smile, even if the medical doctor in her found those things silly. It would be a fun thing to share with Mulder as the baby grew.

  
After she quickly used the restroom, she hurried to change, pulling on her favorite sweater and black pants before making her way towards the guest room. Her heart fell as she stopped in the doorway. Jackson was gone. She should have known that his sudden appearance and presence in their lives would be short-lived, but part of her still couldn't help but hope that they could be a family. Maybe it was too much to ask at this point, but she desperately wanted to get to know him. She sighed. As she turned to leave the room, she spotted the small snow globe that she had taken from his room on the bed. He must have found it, but decided to leave it here.  
  
She carefully reached down and picked it up. A wave of images hit her. A military facility, Jackson walking through the halls, herself and Mulder in a jail cell. Scully braced herself against the wall with her free hand, gasping. Once she caught her breath, she rushed down the stairs. She pulled on her lightweight black jacket and slipped the snow globe inside her pocket. She frantically searched the living area for her keys until she spotted them on Mulder's desk. She had to get to Mulder and their son. From what she saw, Jackson appeared to be helping Mulder escape, but they were both in danger, she knew it. She wasn't quite sure how she would be able to help, but she knew she couldn't lose either of them.

\---

Jackson had slipped out of the house in the wee morning hours and made his way back to his car. His first stop was to Purlieu services to destroy surveillance tape evidence. Using his powers, it didn't take long for him to find the military prison Mulder was at. Once he arrived at the military facility, he focused on the image of another guard who was vacating the facility and projected the image onto himself. The guard at the gate seemed confused at first, but then waved him through.  
  
\---

Mulder blinked against the darkness of the jail cell. His insomnia made it impossible to sleep along with the discomfort of the prison bed. All he could think about was Scully, the baby, and William. He wanted so badly to be a father and he feared that once again he would lose that chance.  
  
Suddenly, he could hear footsteps approaching and he braced himself for the barrage of questioning and possible physical punishment. When he looked up, he saw someone he did not expect to see in a million years.

"Will--Jackson?!" Mulder exclaimed in shock.

"Shh, you have to be quiet," the young man said as he reached into his pocket. 

  
Mulder stood up as Jackson retrieved the keys and unlocked his jail cell. "What are you doing here? You shouldn't be here." The urge to protect his first child was strong. He supposed that's what being father felt like, even though he didn't have the chance to raise his son. When he thought of William, he thought back to the tiny baby he held in his arms seventeen years ago. Now there was Jackson, almost an adult who had these powers that could kill instantaneously. While he was aware the teenager could protect himself, he still felt an overwhelming need to protect him.

"We don't have much time," Jackson said as he looked around. That's when Mulder realized no guards were in sight. 

  
Once the jail cell was unlocked, Mulder startled him by engulfing him into a hug. "I--I saw him shoot you," his voice broke. "Why...why did you take that bullet for me?"

Jackson's head began to throb. He could see Dana on the road and hear her thoughts, which were riddled with anxiety and hear. She was coming to save them.

\----

Scully had to pull off onto the side of the road a few times because of dizziness while on the way to her destination. Her head was hurting terribly and she was afraid she'd have another seizure. The last thing she needed was to get into a car wreck and lose the baby. She was terrified for both William and Mulder though.  
  
Thankfully, she made it to the place she saw in her vision using names of landmarks in order to guide her A military facility. She passed by the large building she had seen in her vision, deciding to park a safe distance away. Scully began to contemplate how she would be able to get in. Jackson was here, she knew it. She felt for her gun inside of her coat and began to slowly approach the facility, keeping her eye out for any signs of danger. She watched a military vehicle enter the facility and a moment later, the booth attendant disappeared. She took that opportunity and hurried towards the entrance. She glanced around for cameras. None appeared to be visible, but she didn't doubt there was at least one hidden somewhere. Hopefully, if she was caught on camera they would be long gone by then.  
  
She was startled by a sudden movement. Someone grabbed of her arm roughly and pulled her backward. She gasped, trying to catch her footing as she turned towards the military officer. "What do you think you're doing?!" He demanded. He had a Russian accent that she recognized. She opened her mouth to respond, but the pain from the death grip on her arm was unbearable.  
  
Unexpectedly, he released his grip on her. "You're good to go, carry on." She watched in shock as he turned away. Confused, she pressed onwards before he could change his mind.  
  
She opened the first door and found herself inside of a dark, ominous looking building. A voice was screaming inside of her head to turn back while she could, but she pulled out her flashlight and kept walking.

\----

Jackson, standing in front of Mulder in the jail cell, hesitated for a moment. "Because..." He wasn't good with conveying emotions. "It's clear that she needs you."

Mulder watched him closely. "You mean Scully," he said carefully.   
Jackson looked away for a moment and then nodded. "And...I kind of just wanted to die. I'm tired of running, you know?" Hearing the teenager he believed to be his son say those words felt like a knife in his heart. He touched the boy's shoulder.

"Don't say that. You don't have to. Not anymore. I killed him...after he shot you."

Jackson nodded. "I know. And that’s another reason." Mulder watched him curiously. 

  
Jackson thought back to the moment at the motel when Mulder first found him. "No one has cared about me quite this much...other than my adoptive parents of course. I know they loved me, even if they didn't understand me."

Mulder nodded slowly. "Your... Scully and I care about you very much."

Jackson smiled shyly, much like he had the first time they met. It reminded Mulder a lot of the Scully who walked into his office twenty five years ago.

Jackson crossed his arms and looked away, appearing to contemplate. Dana was there. He concentrated for a moment, pushing his mind into that of the guard who was bothering her outside before opening his eyes again. Before he could say anything else, the sound of footsteps down the hall started in their direction. He grabbed onto Mulder's arm. "Let's go!"

\---

Mulder followed Jackson into a nearby facility. One that was dark and dimly lit.

"Hurry," Jackson said.

Mulder ran until he heard more footsteps and saw a flashlight pointed in their direction. "Mulder!" Came Scully's stricken cry.  
  
Mulder felt his heart jump into his throat. The sound of her voice was music to his ears. It was heaven. He was terrified he'd never hear it again.

"Scully!" He called back, running faster towards her. 

  
Scully dropped her flashlight and threw her arms around him. She was small, but her grip was so tight that he could barely breathe. Her body began to shake and that was when he realized they were both crying. He reached down to capture her lips with his own. All was forgotten in the moment. They pulled back a minute later and Mulder placed his hand on her abdomen. "You and the baby are okay?" He asked looking down at the small swell. The relief he felt seeing that she was unharmed was indescribable. He was terrified he would never get to see her again this time.  
  
Scully nodded quickly through her tears. "We're fine," she assured him. I was just so afraid I'd never see you again," she looked up at him. Tears had stained her cheeks.

"I know me too. But Jackson helped me," Mulder said. They had been so lost in the moment that they had temporarily forgotten about Jackson. They both turned, only to realize they were alone.

"Will..Jackson!" They both cried.

Both of them frantically looked around and down towards the staircase. It was dark and they couldn't make out much. Scully moved to run onwards, but Mulder stopped her.

"No don't, Scully!"  
  
Scully looked up at Mulder, pleading. She regretted the words she uttered on that dock about William. He was theirs and they would prove it. "I can't lose him again," she pleaded.

Mulder gripped her shoulders and pulled her to him. "He can protect himself in a way that we can't, Scully."

Scully looked back at him in confusion as he continued.

"I got to talk to him, Scully. He wants to help us and I know he'll find us again when it's safe."

Scully sighed. She knew he was right. Her son had survived a bullet wound to the head. He had powers that she couldn't begin to comprehend.

"I know, I just...I couldn't help but hope."

She didn't have to finish that sentence for Mulder to know what she meant. He wanted their son to come home with them too. And maybe someday, he would.

"We're going to see him again, Scully. He risked himself to help us, he wants to know us."

Scully nodded tearfully, holding onto that thought as she wrapped her arms around Mulder once again, trying to keep herself together. She felt his arms tighten around her and she reveled in the comfort of his embrace.  
  
Suddenly, another small flutter in her abdomen startled her and caused her to gasp out loud.

"Scully?" Mulder asked, alarmed.  
  
Scully reached for his hand like she did when she first told him about the baby and brought it to rest on her stomach. "I can feel her," Scully said, her voice thick with emotion. 

  
Mulder stared back at her, mesmerized.

"You won't be able to feel the movement just yet, it's still early. I just started to feel her last night."

Mulder rubbed the spot where Scully rested his hand, hoping the baby might feel his touch.


	10. Chapter 10

**Summary for the Chapter:**

> Thanks to MonikaFileFan for helping beta this chapter!!

Mulder followed Scully close behind as they made their way out of the building. He stayed close to her, trudging along despite the injuries he sustained while being held captive. Though he knew she was fully capable of protecting herself, he would be damned if any harm came to her or the baby. Finally, they reached the car and he noticed by her faltering step that she was tired, both physically and emotionally as much as she tried to hide it. "I'll drive," he said reaching for the keys. 

"Like that?" She asked skeptically, eyeing his orange outfit. He sighed and shrugged the top off. 

Thankfully, he had a white shirt on underneath. Tossing the orange shirt to the side of the road, he took the keys in Scully's outstretched hand. 

  
Scully let out a long breath as they got into the car. "William, he....destroyed the surveillance footage and anything tying you to those murders." 

Mulder stepped on the gas anyways but regretted it when Scully gasped and braced her arm against the door. "Sorry, I know. He may have had a troubled life, but he's a good kid." 

Scully reached into her coat pocket and examined the windmill snow globe. "He came to the house last night...after you were taken." 

Mulder looked over at her in surprise. 

"He said he could help you. We didn't talk about much else. It was unreal…he thinks the baby is a girl." 

Mulder's features lit up at that. "Really?" He couldn't help but imagine a little girl that looked just like Scully. He'd always wanted a daughter to protect in a way that he couldn't with Samantha.   
  
Scully smiled. "I don't know why, but I'd have to agree with him. It's just a feeling I have." 

"Ah, maternal instinct?" 

"Something like that.”

  
Mulder watched as she toyed with the snow globe in her hand. "You really like that snow globe, huh? Maybe I should have taken a few more for you. I'm sure he wouldn't mind," Mulder teased.   
  
Scully smiled. She had the most beautiful smile and she was even more beautiful with that pregnancy glow. 

"It's the only tangible thing of his I have aside from those photos." 

Mulder reached for her left hand and clasped it tightly, sensing her affliction. "He'll be okay, Scully."

\---

After several glances back to ensure they weren't being followed, Mulder pulled up the graveled driveway of their home. Home. He was afraid he'd never see it again. He looked over at Scully, who had dozed off at some point. She looked up as he killed the engine and they both got out of the car in resignation. Mulder was eager to burn the orange pants in the fireplace later.   
  
Times like this were when Scully yearned for some coffee. It was still early in the day, but they were both exhausted and trudged up the stairs. Scully stopped by William's room and reached into her coat. She set the small snow globe back in its proper spot on the shelf. 

As she turned to leave, she noted the neatly made bed. He was definitely her child. That was when she noticed a small piece of hair on the pillow. It was dark and too long to be Mulder's. Then she got an idea. 

"Scully?" Mulder asked from the doorway. He has already changed into a t-shirt and sweats. 

"I need your hairbrush, Mulder." 

He gave her a confused look. "Why?" And then it dawned on him. "Scully..." 

"He's our son, Mulder," she said without hesitation. 

"He is your child, Scully. Like Emily was. I wouldn't hesitate to be a father to her either." 

"No Mulder, he's  _ ours. _ " 

"But you said--" 

"I was wrong. I shouldn't have believed him. The smoking man is a liar. A master manipulator. Do you remember when we did the IVF and it didn't take?" 

Mulder nodded. The news was devastating and they had made love afterward, finding comfort in one another’s arms. 

"We later found out those doctors were involved in creating alien hybrid babies and then taking them from their mothers’ wombs. They weren't to be trusted,” she explained, pacing anxiously.

Mulder shook his head as Scully walked closer. "What are you saying, Scully?" 

She paused for a moment. "What if it didn't take, because there was nothing to take? What if it was a cover-up? A violation of our fundamental human rights?" 

"Scully, are you saying you think they took our specimens and used it for their own sick, twisted agenda?" 

Scully nodded. "It's the only way I can explain it. I ran so many tests on William when he was a baby, but I didn't doubt that perhaps another hand had been involved. I didn't want to believe there was any outside involvement in his conception"

Now it was Mulder was afraid to hope. He still considered William his son as he was still Scully's child without question, just like Emily. Still, he was afraid to relive that soul-crushing revelation. He knew Scully was heartbroken, just as much as he was. He didn't want her to get her hopes up either. 

"Okay," he nodded. “What did you have in mind?”

"I have a friend who owes me a favor at OLOS." 

Mulder placed his hand on Scully's shoulder. "Tomorrow," he said as he assessed her tired features. "You should rest, Doc." Mulder smiled. 

  
Scully sighed, knowing he was right. Just then, she felt the vibration of her phone in her pocket. It was a text from Monica. 

"What is it, Scully?" Mulder asked as he watched her expression as she looked at the screen. 

"It's Monica," she said. "She found John and they're going to come back to D.C." 

It had been ages since Mulder had seen either of them…if you didn’t count the near-death encounter. 

Though he had questioned Monica's motives, he trusted Scully's judgment of her character. She was in a similar predicament as Skinner had been in with the smoking man, yet Skinner never failed to help them. Scully, William, and the baby were safe because of them and he was forever grateful for that.


	11. Chapter 11

**Summary for the Chapter:**

> Many thanks to Monika for beta-ing this!

Scully felt warm and safe in Mulder's arms as he held her in the bed they shared for many years. His hand was productively curled around her baby bump. It had been a long time since he had held her like this, spooned right behind her. When they had separated, she had missed that familiar warmth and intimacy they once shared for so many years in this house. Her smart house might have had all the latest fancy technology, but it never felt like a home. If someone had told her a year ago she'd be living with Mulder again and expecting another child, she would have laughed them out the door.   
  
But here she was and she wouldn't trade any of it for the world. She only regretted fleeing when things got difficult when Mulder became depressed and allowed it to consume him. In the past year, she realized how much that had changed. How much  _ he _ had changed. His patience was unremarkable and he always put her needs first. Though he was always passionate about their recent cases, he was more reserved and cautious, yet still that brilliant and handsome man she met 25 years ago.   
  
Scully had changed also. She had allowed her guard to drop around him and allowed him to see the most vulnerable sides of her. Going to his room in the middle of the night on that doppelganger case was what landed them in the present situation she thought with a smile. Admitting fault for their separation and William was also difficult. She still felt like she had failed William. Was he okay? Was her unborn baby different? What if she couldn't protect her? Part of her felt like she didn't deserve this little miracle that was growing inside of her. 

"Scully?" Came Mulder's groggy voice. 

"Hmm?" 

"What's wrong? I can feel you thinking." She sighed. 

"I'm worried," she admitted. She knew he wouldn't be satisfied with an 'I'm fine' and communication is what made relationships work, so she was determined to make things right. 

"Hmm. Talk to me, Dana," he urged.

Scully moved to face him and she placed her hand over his. "What if something goes wrong...with the baby? I already love her so much, but I'm afraid I might lose her too. We're in our fifties and the odds are against us." 

Mulder looked at her with genuine concern. His eyes were full of love. "Oh, I see. Well, we've survived worse odds, Scully. And we've had stranger things happen, so parenting in our fifties would be a walk in the park." He moved to tuck a strand of hair behind her ear. "And you won't lose another child. I promise. We won't lose her," he said as he stroked the small bump with his thumb. "I'm here and I'm not going anywhere," he assured. "Not this time." 

Scully managed a small smile as she fought back the tears. "And William--he can't be out there all alone. I know he knows that I love him, but I want him to know he has a home." 

Mulder thought back to the night at the motel where William said everything was all his fault and that he would have been better off dead. It was like a knife in his heart. Whether the depression was hereditary or as a result of everything he had been through, he wasn't sure. 

"I'm so sorry, Mulder. I'm so sorry I left when you needed me. I failed you and I failed William," she began to sob. Her words brought him back to their recent conversation in the church.

Mulder pulled her closer to his chest and moved to wipe away the single tear that made its way down her cheek. She recalled her mother's last words and wished she was here. 

"You have to stop blaming yourself for everything, Scully. Those things are in the past. You did what you needed to in order to protect him. You gave him a happy childhood. A life on the run wouldn't have been any life for a child and he knows that too." 

"I got to hold him, Mulder. Oh God, he is so much like you." 

"He is pretty amazing, huh?" Mulder kissed the top of her head as he hugged her trembling body against him. He was glad Scully finally got a moment with him. She deserved that much.   
  
Scully smiled and cried into his chest until she fell asleep.


	12. Chapter 12

**Notes for the Chapter:**

> I know it's been a while since my last update, so I hope you guys enjoyed these three chapters. :)

Jackson managed to escape the military facility after leaving shockingly few casualties behind and leaving all the personnel confused in the process. His next visit was to the FBI headquarters that night to erase any physical evidence pertaining to Mulder. Dana and Mulder really loved him. He knew that much. Sometimes it hurt especially to see the pain and sadness in Dana's eyes, but he also saw love. It was the same love he felt in the visions they shared. She had the same love for him as she did the baby inside of her. He felt a connection to that tiny life too. It was how he suspected she was pregnant and then he shared that vision with her.   
  
After manipulating a few different people, he made his way into the FBI headquarters. His first stop was to the director's office. The office was dark and there were no signs of life. He opened the laptop on the desk and began to wipe the computer of any evidence to Mulder's incarceration. Before he did, however, he located a file titled "Project Crossroads". He clicked on the file and noted it was passworded of course. It didn't take long to hack it, but it was longer than he anticipated originally. He didn't have much time, but the names Dana Scully and Fox Mulder along with "specimen" piqued his interest. He has read quite a bit on Project Crossroads. He had learned a lot about himself and others like him that way, but he hadn't seen this one before. He transferred the file into the thumb drive attached to the computer and then wiped the files on Mulder.

\---

Scully had dropped off the DNA specimens to her colleague a few days ago and it would be ready any time now. The first time she was able to get results within hours due to the special circumstance when she thought her son was dead, but that wasn't typical unless there was a genuine reason for the rush. 

  
Amidst their anticipation of the results, this was also an important and exciting day for both of them as they were going to see their baby for the first time. They both sat awkwardly in the OBGYN office before Scully was called back. Mulder followed with his hand on her lower back. He knew Scully felt self-conscious about being the oldest expectant mother in the room even though more and more people were having children later in life these days. Scully always looked radiant to him and he loved seeing the changes in her body as she nurtured their child since he hadn't been around for much of her first pregnancy.   
  
A nurse had taken her weight and blood pressure before they were led down the hall.   
  
Scully turned to look at Mulder, smiling anxiously as they were led into an exam room equipped for the ultrasound. Mulder took Scully's hand and gave it a light reassuring squeeze. The nurse instructed Scully to lay down on the exam table said the doctor would be in shortly.   
  
Scully was wearing a dark blue knit sweater...it was one of her favorite things to wear these days as it was comfortable and hid her growing belly. She wore more fitted clothes at home because Mulder admittedly wanted her to show off the changes in her body. Seeing the excitement in his face knowing they would see their baby for the first time, brought tears to her eyes. He never got to experience this with her before and she was glad to finally get to experience it with him. It was a bittersweet moment with William, seeing her baby while knowing Mulder was gone. Now he would be here for everything.

A Dr. Andrews had come in to introduce herself. She and Mulder had done heavy research into finding a reliable and trustworthy doctor. "Hi, Dr. Scully, how are you doing? This is your...second pregnancy?" She asked, glancing at the chart in her hands. Scully nodded. 

  
Dr. Andrews asked a few questions about Scully's health before they got started. "While it is uncommon and rare to conceive naturally at this stage, it isn't impossible. I looked over your medical history and in your case, it is a miracle, but miracles do indeed happen," she smiled. 

She asked Scully to lower her pants slightly and pull up her sweater. "Now, let's see how that baby of yours is doing.”

  
Mulder watched as the doctor applied some cool gel on Scully's rounded abdomen. He took her hand in hers as they watched the screen. Dr. Andrews moved the wand until the little blob that was their baby appeared. "There's your baby," she said with a smile. 

Mulder squeezed Scully's hand as both of them looked in awe and amazement. "There's our little blobfish, Scully." 

Scully looked at him and smiled, eyes full of tears before she turned back to the doctor. She felt a sense of dread settle over her as she noticed the doctor’s change in expression. "What's wrong?" Scully asked, suddenly alarmed. 

Mulder moved closer, gripping her hand tightly. That was when she realized the lack of a sound of a heartbeat.

"Ah, there it is." The doctor moved the wand lower and both let out a sigh of relief as a small thumping sound filled the room. It was a wonderful sound. 

"Baby just didn't want to cooperate. But we have a good, strong heartbeat. You're about fifteen weeks along now, which is excellent. I know I don't need to tell you, but your chances of miscarriage are much lower after the first trimester. Unfortunately, only about 20% of pregnancies after age 48 make it to term, but seeing how far along you are already and your being in excellent health, I see no reason why everything shouldn't be just fine." Scully and Mulder nodded.

Scully looked over to see the tears in her partner’s eyes. "The baby is moving quite a bit already, you can probably feel quickening movements already." 

Scully nodded. "Yes, I started to feel them a few days ago."

"I have a note to do an amniocentesis today," Dr. Andrews said. "I know you're also a doctor and understand the risks, but I'd also highly advise it given your ages." 

Scully nodded. "We can also tell you the gender once we have the results. Would you like to know?" 

Scully looked to Mulder who smiled in agreement. "Yes," Scully said as she turned back to the doctor. 

Dr. Andrews had Scully sign a consent form. "You didn't find out about the pregnancy until recently, correct?" 

Scully nodded. "I just thought I was gaining weight honestly and I figured my other symptoms had to do with menopause." 

The blonde doctor smiled. She was about Scully's age if she had to guess. 

"Well, that's completely understandable. Your baby looks just fine. Until we get the results and decide otherwise, I'd suggest a twice-monthly checkup just as a precaution." 

Mulder's gaze was still fixed on the image of the baby and the sound of its heartbeat. 

"I will print out some photos you can take home." 

They did the amino next and Mulder had to look away once he saw the large needle and the doctor putting it into Scully's abdomen. Those needles were associated with many terrible memories. 

  
Once she was finished, she wiped off the gel and Scully sat up as the doctor explained limitations of activities since her pregnancy was a high risk one. "Did you have any complications with your first pregnancy?" 

Scully sighed. "I had a partial placental abruption." 

Mulder frowned at the memory. He had been terrified of losing them both.   
  
Dr. Andrews jotted some notes down on a piece of paper. "Okay, that's definitely something we'll want to monitor." 

Once they were finished at the OBGYN, Scully received a phone call that the DNA results she had run were ready. She was glad she choose a doctor outside of her hospital to monitor her pregnancy. The hospital she worked at was small and people talked. She didn't want many people knowing about the baby just yet though she didn't have much longer before it would be pretty obvious. She was already showing some but did her best to hide it while she was out. She knew she looked younger, but she didn't want to deal with the looks and judgment of having a baby late in life.   
  
It didn't take long to reach her hospital and to her surprise, Skinner was also being released that day. She hoped they would catch him before he left. Mulder followed Scully to her shared office space. Neither could believe it had been nearly two years since she had worked here full time. She was on an indefinite extended leave, but somehow they still managed to leave her space since she hadn't given an official resignation. Thankfully, no one was in the room once they entered and a yellow envelope with the results had been left on her desk. They locked the door behind them.   
  
Mulder's hands grew clammy as Scully opened it and examined its contents. He wasn't a doctor, so he didn't bother to try and read what it said and instead watched her face. Once he saw her lips quiver and the tears filling her eyes, he sighed. 

"Scully," he started, not wanting to relive the rejection all over again. He didn't want that for her either, especially now.   
  
But suddenly, she smiled as she let out a sob and threw herself into his arms. "He's your child, Mulder," she cried into his chest. "He's ours and he's going to have a sibling." 

Those words were magical to him and he wrapped his arms tightly around her, breathing a heavy sigh of relief he hadn't realized he'd been holding. He had wanted to believe and finally, that cloud of darkness had been lifted.


	13. Chapter 13

Once Scully and Mulder had gathered themselves to leave Scully's office, they caught Skinner in the corridor. "Sir," Scully said as they caught up to him. As Skinner turned towards them, they recognized Arlene walking towards him. He was using a walker temporarily and would progress to simply needing a cane. 

  
Skinner looked surprised to see them. "Agent Scully...Mulder." From what Skinner heard Kersh had poor recollection of recent events and even offered him his position back. The X-Files was still done for though. Kersh still remembered Mulder had made headlines and it earned the FBI a bad reputation. It was time for him to retire though. Scully walked closer, happy to see he was on his way to recovery.

"You're being discharged?"

  
Skinner nodded. "Yeah, I'm ready to get out of here. I still have some rehabilitation therapy ahead of me, but it is what it is," he shrugged, probably just happy to be alive at all.

"Let us know if you need anything?" Mulder urged.

"I think I'll be fine, Agents...former agents," he nodded at Arlene who smiled at them.  
  
Mulder and Scully shared a knowing glance. "You know where to find us,"

"Come over anytime, Skin man."

Skinner leaned in to whisper Mulder's ear. "Don't screw it up this time. You're a lucky man," he said tersely. 

  
Mulder nodded slowly. "Thank you...for being with her," he whispered. "Even if we didn't trust you."

Scully eyed them suspiciously.

"What's going on?" Scully pressed.

"Oh nothing, just giving my congratulations," Skinner winked at Mulder.  
  
Mulder moved to stand next to Scully as Skinner walked towards Arlene who touched his shoulder tentatively. Scully took Mulder's hand and they smiled as they watched the two depart.

\---

The following weeks were spent cleaning up the house and starting work on the nursery. Scully was now twenty weeks along and they had found out not long after her first ultrasound that they were having a baby girl. She sighed as she absently rubbed her rounded midsection. This was her second pregnancy and there was no more hiding the evidence as she began to show much sooner than before. 

Though they weren’t separated long, she was growing used to being back here. This house held a familiar comfort that was lacking in her oversized apartment. Aside from the Purlieu incident, they had always felt safe here. Mulder had taken it upon himself to install a thorough security system afterward that they both could monitor from their mobile phones. They could hear and see people approaching and ringing the doorbell from anywhere they were with the cameras around the outside of their house.

  
They heard nothing more from Kersh or Purlieu. It was as if nothing had ever happened. It was bizarre, but Scully was just thankful she had Mulder here with her. She wouldn't be able to do it on her own again, especially at her age now. Everything was absolutely perfect aside from missing William, though she sensed she would see him soon.  
  
The sound of her phone startled her from her thoughts. Monica had been texting her the past few weeks. She and John Doggett were on their way back to D.C., permanently. John had also been undercover, which explained why she hadn't been able to look him up either. Things seemed to be going well for the two of them and she was happy about that. They found their way back to one another much like she and Mulder had.

"Scully?" Mulder called from his office.  
  
Scully moved towards his office, noticing for the first time how gravity was starting to shift with her increased girth. His office looked much like it had when they had first lived together. Newspaper clippings on the wall and pencils already back up in the ceiling. She folded her arms over her stomach.  
  
She smiled and regarded him with a raised brow. "What, Mulder?"

"Here," he said, pointing to the screen of his laptop.

She regarded him skeptically before peering at the screen from behind him.

"It's perfect for our blobfish," he said.

Scully couldn't help but laugh. On his screen was a tiny onesie with the same skeptical looking fish that was on Mulder's dinner plate at that questionable sushi restaurant from a few months back. "Mulder...seriously?" she teased.

It actually warmed her heart that he was spending so much time looking for baby things to complete her nursery.

"You don't like it," his face fell.   
Scully shook her head as he snuck his arm around her waist, pulling her closer to him.

Mulder reached out and placed his hand over the swell of Scully's stomach. She covered his hand with her own.

"No, I love it, Mulder. We just need to figure out a name for her other than blobfish. She's already going to get teased at school for having old parents."

Mulder smiled at her approval. He pulled her closer and kissed her belly.

"What do you think, Blobfish?" He said.

They both had started talking to the baby in recent weeks. Scully had explained that babies can hear outside the womb at about sixteen weeks gestation and can recognize the voices of their parents once they're born.  
  
Scully felt the baby shift and Mulder gasped at the sudden slight movement under his palm.

"She moved," he beamed, stroking the spot. "I think she likes it."

Scully felt tears well in her eyes. She had been feeling her move quite a bit, but it hadn't been distinguishable until now.

"Walk with me, Mulder," she said. "I've been in the house too long."

"Uh oh."

  
She smiled reassuringly and took his hand as she guided him out of the office. "You could use some air too, you've been in here all day."

"Have you thought of any names while doing your research?" Scully asked.  
  
Mulder held onto her hand as they eased down the steps and onto the pathway in the front of their home. "Well, I always figured if I had a daughter her name would be Samantha, but I think she should have her own name. Something untied to the darkness of our past."

Scully nodded as she enjoyed the warmth of the midday sun. "Melissa is probably out then. I thought about Margaret, but you're right, maybe it's best...no family names. She should have her own name. I know my mom would have loved a granddaughter though," she thought wistfully with a twinge of sadness. 

  
Mulder squeezed her hand. "She would have loved her. I'm confident she's watching over her though."

Scully was impressed. "Mulder, believing in God? I'm impressed. I never thought I'd see the day."

Mulder shook his head and chuckled. "Not God. You, remember? Anyways, I was thinking we could call her Kit."

"Kit?" Scully asked incredulously. "Says the guy named Fox who insists on going by his last name."

"Well, Katherine if we're being technical. With a K."

"My middle name?" Scully asked in surprise.

"Yeah, does it have any personal significance?" He asked. They had known each other twenty five years and they had never had this discussion.

"Actually it was after my great aunt. It means pure. There are many variations of it though. Poor kid will be spelling it out all the time."

"So is that a yes or a no? Do you like it?"

  
"A baby Fox," Scully mused. Scully felt the tears coming, bless those damn pregnancy hormones. She came to an abrupt stop on the pathway, taking his hands in hers and pressed them to her belly.

"How about that, little Kit?" She said.

"She'll probably want to go by something like Kate or Katie at school," Mulder shrugged. "But she'd be our little Kit."

Scully was practically crying. Mulder gently pulled her into his arms.

A minute or two later, Scully was finally able to gather herself.

"So, other than family names, is there anything else you considered? You can't tell me you never had a favorite name growing up."

"Well, to be honest Mulder, I didn't. I never really thought about getting married or having a family until I was much older...until," she was unable to say the words.

Until she found out she couldn't have a child. And yet, here they were.

"Well, when I was pregnant with William, I frustrated the hell out of my mom by not telling her when I found out I was having a boy. We talked about baby names and she initially suggested naming the baby after Missy if it was a girl but said I should also consider Lily or Lillian. I wish I could tell you why she suggested those names, but it's just as much of a mystery to me as that quarter. I'm pretty sure she was trying her best to make me slip up on the baby's gender."

Scully looked away slightly, feeling another sudden onslaught of tears.

Mulder took her hands in his.

Gathering herself, she turned back to meet his gaze. "I want you to pick her name this time though."

"Well, then I think we have a winner. Katherine Lily Scully-Mulder. I want to make sure she has both of our names too."

Scully nodded. She wanted this child to have Mulder's name. This time she wanted no ambiguity. They had found out as soon as they were able that they were having a girl and she would also have Mulder's last name.

"I know we haven't been conventional people, but I'm so happy you're on this journey with me, Mulder." Mulder rested his head atop hers.

"I know. And I may not be the best communicator, but thank you, Scully. I couldn't imagine a better Father's Day present. Thank for giving me this second miracle."

Mulder thought back to when she told him he was a father on that dock during an ungodly hour of that fateful night. He had been crushed losing William and the news that she was expecting, as impossible as it was, filled him with hope. The moment she brought his hand to her belly, he knew he already loved the tiny life inside implicitly.  
  
Scully pulled back for just a moment and smiled, her eyes full of tears. She looked up to see them in Mulder's eyes too. She reached up and pulled him towards her, locking her lips with his. 

  
She suffered for many years, knowing she had made the decision to give up William without him. The pained agony in his face as he suffered once again the loss of fatherhood and loss of purpose in his life had shattered her. It wasn't a look that could be unseen and she hoped she'd never had to see that look again.

It wasn't how she wanted to tell him about the baby, but she was glad she could save him from falling into another depression. They were going to be a family. She had proof that both children were theirs and no one would ever take that away or make them fear otherwise again.

A/N: I wrote this part during Father's Day, hence the Father's Day reference. :)

**Notes for the Chapter:**

> I've seen so many wonderful names for baby #2. I've had a difficult time coming up with one canon name for her. I had people vote on a name on Instagram and the result was Katherine, because it makes sense for Mulder to call her "Kit", a baby Fox. In the past I've named her Alethea, Vera, Gracie, Micaela and Melissa. But the fans seem to agree no Samantha or Melissa for #2. I've also been seeing Lily a lot and love that one as well, so I ended up settling for Katherine Lily.


	14. Chapter 14

Once they had eaten dinner, both of them had settled down to watch a movie and ended up falling asleep. The combination of both age and for her, the pregnancy, was wearing them out. Scully woke with a strange feeling—a sense of loneliness, only it wasn't her own. 

Mulder was sleeping peacefully right beside her. She wasn't sure how she knew, but she sensed William's presence close by. Almost as if he was reaching out to her. Intentional or inadvertent, she wasn't sure. She quietly got up from the couch and smiled lovingly at Mulder as she watched the rise and fall of his chest.   
  
She quietly sneaked out of the back of the house as to not wake Mulder. The sky was darkening as she walked down the steps and around the back to the small trail that led to the vast acreage behind their house. Sure enough, she approached a hooded figure sitting on the grass with its back towards her. In any other circumstance, she would have drawn her weapon. But she knew this person wasn't a danger to her.   
  
She stopped just a few feet away and sure enough, Jackson turned towards her.

"Hi," she said. Her voice trembling. Her arms ached to hug him.

"You found me," he said with a grin.

"Well, it seems like you wanted me to," she said, easing herself down on the grass beside him without permission. 

  
Jackson looked over at Scully as she sat next to him. She had a hand cupped around her belly as she sat down. The baby had gotten bigger, he couldn't help but notice.

"Thank you," she said. "For helping Mulder," her voice wavered.

"It's okay," he shrugged. "He was kind of in that mess because of me."

"You're our child. I know we didn't get to raise you, but he loves you. We both do. You don't owe us anything, it's what parents do."

Jackson managed a small smile. The thought of his adoptive parents made him sad. They were gone because of him. He hadn't even bothered to find where they were buried. Maybe Dana knew, but was it safe?

"It's my fault though. My parents...they're dead because of me. I don't want to lose anyone else."

"Honey," she said without thinking as she reached out and touched his shoulder. "None of this is your fault."

Jackson had done his best to keep walls up around others, but with her, it was different. He felt the walls around him slowly coming down. "I'm so tired of running, of being a freak...of being alone,” he stiffened, hugging his legs close.

Scully felt the air leave her lungs before she could speak. She had never wanted this for her son. Knowing she had failed him felt like a knife to her heart. She tightened her grip on his shoulder, willing him to look at her. "That isn't true," she said. "And...it doesn't have to be that way. You're always welcome here," she told him, not wanting to push him too much. 

  
Jackson looked away and seemed to consider. He was conflicted. He was tired of being alone but afraid of putting them in danger. "There is something else," he said. "I always thought the guy I saw in my visions was my father...the old smoking man. But I found something," he said as he reached into his pocket. He handed Scully some papers on the Crossroads project and waited as she looked them over. The papers contained pertinent information on the details of the experiment they were part of. Specimens were taken from both Fox Mulder and Dana Scully for the project.

A moment later, she was crying again. "I know, I....we ran some tests recently to be sure," she explained. Seeing it on paper was the validation she needed aside from the DNA test.  
  
Jackson had been utterly relieved such a horrible person wasn't his father. How could he have not figured it out sooner? Why did he not have the same connection with Mulder that he did with Dana and the baby?   
  
As if on cue, the baby had moved and he looked over at her as she startled in surprise, placing her hand over the baby.

"You knew it was a girl," she said suddenly. "You were right."

Jackson was impressed with himself. "It's hard to explain, but I can hear her too. Does it hurt?" He asked with genuine curiosity.

"No, not yet," she said with a smile. "But as she gets bigger, it might sometimes."

He watched her curiously with a question in his eyes.

"Here," she offered, reaching for his hand.

He awkwardly allowed her to bring his hand to her belly. Sure enough, he could feel the small, but distinguishable movement coming from inside.

"Wow," he stared at her in amazement. Scully had tried to keep her pregnancy a secret for as long as she was able with oversized clothing, but that was nearly impossible now. 

  
Normally, she was very protective when it came to the baby and she didn't want unsolicited attention from strangers. 

  
Mulder was the only one she was comfortable sharing and talking about the baby with until now. She wanted her son to know about his sister and feel he had a place with them.  It was important to her that he knows he wasn't being replaced.

"Did...I move a lot too? When I was a baby?" He asked tentatively as he turned to stare at the grass. He wasn't used to personal conversations like this, but he found comfort in talking to Dana. When he talked to her, it was as if his fears temporarily vanished.

"Yes, you did. A lot actually. I was going through a particularly difficult time when I was pregnant with you," she started to explain. 

  
Jackson sensed that was a later conversation and didn't push.

"It's a long story, but knowing I was having you was a great comfort. Especially because I had learned not long before that I couldn't have children."

Jackson nodded. The word "experiment" still hung around in his thoughts still. It hurt to know that his birth mother had been used and violated in this way.

"But, isn't it different now that you know how I came to be?" He couldn't help but ask. 

  
Scully stiffened. The knowledge of being violated was still something she struggled with, but she didn't want her son to see that.

"You're still our child. That's what's important. No matter how you came to be." It was true. Test tube or no, he was still their biological child.  
  
She shifted slightly, growing uncomfortable as she sat on the grass. Her legs were tingling and the baby's weight was pressing on her bladder. "Why don't you come inside? I'm sure Mulder would love to see you. Please?"  

Scully’s chest felt heavy as she awaited the answer, afraid to hope, but also terrified of pushing him away in the process. She wanted so badly to get to know him and she couldn’t help but feel that part of him wanted to know them too.

Jackson hesitated for a moment before nodding. "Okay," he relented and they both moved to stand. He reached for her hands and she allowed him to help her up.


	15. Chapter 15

Recovery had taken less time than the last. His alien DNA had always proven useful and never failed him. His idiot son hadn't even thought to put a bullet in his head to finish the job. Even more importantly, how could he have not seen it was William he had shot? That was something he hadn't expected. He sighed, crossing his legs as he lit his cigarette. 

  
Carl really missed having someone to light his smokes. Monica Reyes..he would make her pay for her betrayal. He had suspected it when she placed the call to Mulder and Scully and trying to bail when Skinner approached him in the alley confirmed that suspicion. She had led them to William. It was laughable that Skinner had shot her, ironic almost. However, he knew Reyes possessed similar alien properties that he did. It was part of their deal. Skinner also paid the price for his betrayal...until he had gotten word the man was alive. He cursed himself for not stopping to check his pulse.   
  
He had recently sent a spy to Mulder's house. It didn't take long for him to figure out William was alive. It wasn't a surprise, it made the boy all that more special and desirable for his plan. The least he expected of all of this was that Dana Scully was pregnant and without any intervention. Perhaps the junk alien DNA had become active and restored her fertility. That child would also be protected inheriting her alien DNA.   
  
Holding a vial in his hands, he vowed to finish his job.

\----

Jackson was glad he made the decision to go inside. Mulder was happy to see him, he could tell. He hugged him tightly and he didn't fight it. He had said this was the best Father's Day he had ever had because he had never really had one before. It was extra special because he was with them and they were expecting another baby. 

  
Dana had suggested having dessert after they had given Jackson dinner. Mulder teased her about craving Jell-O. There was a story to that because she was craving a particular type of Jell-O. She ended up making simple strawberry Jell-O to satisfy her craving. Watching her hungrily consume the Jell-O was amusing. Weren't pregnant people supposed to crave ice cream and pickles? 

  
Dana told a story about Goop-O ABC, a story Mulder had apparently heard before and suddenly that story led to talking about a case of theirs that involved parallel universes and the Mandela effect. Mulder sadly reminisced on a favorite TV show called The Lost Martian. "It's not parallel universes!" Dana had said. This led to playful bickering between the two of them and it made him long for his adoptive parents.   
  
It had been a difficult day for him, remembering his adoptive father, but he felt happy with Mulder and Dana. He hadn't felt content quite like this in a long time. Part of him felt slightly guilty though.   
  
As if sensing his thoughts, Dana placed her hand on his shoulder and smiled. 

"Do you know where my parents are buried?" He asked suddenly. He felt guilty he hadn't thought of this before, but he had been too busy running.   
  
He saw a flash of pain across her face, but it was gone in an instant. "Yes, we can take you to visit them if you'd like. We made sure they were honored properly." 

Just as they were establishing comfortable ground with one another, Jackson was gone again. They planned to bring him to where his adoptive parents were buried, but suddenly something was off. Scully could tell because the next moment he said he had to leave suddenly. 

  
It broke Scully's heart as it usually did. She couldn't quite get used to him entering and disappearing from their lives on a regular basis. So she cried in Mulder's arms, as she usually did these days thanks to dreaded hormones. "He'll be back," Mulder soothed. 

  
Still, Scully couldn't shake the feeling that something wasn't right.   


**Notes for the Chapter:**

> **runs** I know bringing back CSM probably has you reeling, but please hang in there. I only did so because I felt his death was too ambiguous in MSIV. I mean Mulder had to PUSH him into the water after unloading his clip into the man's chest. My goal with this story is to give a more satisfying send off than what we were left with.


	16. Chapter 16

**Notes for the Chapter:**

> Enter Doggett and Reyes...we really lack stories with them these days. I brought Doggett into the fold since we never got to see what he's been up to. Mulder and Scully need more friends and confidants. And Scully especially deserves a female friend.

The following night, Scully prepared dinner for Doggett and Reyes with Mulder's help of course. She had been feeling more fatigued as the pregnancy progressed. Being a much older expectant mother didn't help even though she wouldn't change it for the world. It worried Mulder, but she had assured him she was fine. He wasn't entirely convinced by that of course, but she insisted that he would know if something was wrong, for the sake of the baby. 

  
Scully was anxious and excited to see their friends again, especially Doggett. She hadn't seen nor heard from him in years. She was fortunate enough to see Monica before she left the hospital.   
  
Mulder could tell something else was weighing on her mind, about William, he had assumed. She didn't elaborate and he didn't push the subject.   
  
They arrived promptly at six and Scully and engulfed both her friends in a warm hug. 

  
Mulder was right behind her. He reached out to shake Doggett's hand, but John pulled him into a friendly embrace. Staring back at one another, it was as if no time had passed. John Doggett had filled out some, though he wasn't overweight and his graying hair only made him look more sophisticated. 

  
Mulder had only seen Reyes for a moment before she was transported to the hospital, but she was looking well and thinner than he remembered. "Mulder, Dana...gosh, it's been so long," Doggett said as he smoothed his hair back.   
  
Monica looked around their porch, admiring the surroundings of their country home. "We almost got lost coming here," she laughed. "You really made sure no one could find this place." 

"That was the idea," Mulder said with a grin. "Though Scully hated the commute to the hospital." 

"We fell in love with it when we saw it," Scully said wistfully.   
  
It was then that Doggett's gaze settled on her abdomen. She didn't make much effort to conceal the evidence of the pregnancy at home, so her twenty-week belly was becoming hard to miss. "Wow, Dana....umm congratulations?" He said in shock. "This was definitely an unexpected surprise."

Scully's hand instinctively went to her abdomen. She looked over at Monica, who shrugged. Doggett turned to her. "You knew about this already?"

Mulder was relieved that Doggett and Reyes' visit had brought a smile to her face. Ever since William had left so abruptly, the melancholy hadn't escaped her.  He was worried about the effect of William being in and out of their lives would have on her.

They ate and then talked for hours, about recent events, the baby and what was next for all of them. 

Doggett talked some about his recent undercover assignment. It reminded them both of their temporary case in Arcadia. 

"I still cannot believe that smoking sonofabitch survived a missile strike. Mon and I saw it," Doggett shook his head. 

"I emptied my clip into him after I saw what he did to William. He's done for. I made sure of it," Mulder insisted.   
  
Doggett was still wrapping his head around Reyes' assignment, but she had insisted she had done it to protect William and Scully. In that way, she had succeeded and he supposed that if he were in her position, he might do the same thing.   
  
He felt for Dana and Mulder having to relive losing William, even if he wasn't dead.   
  
They talked some about William's abilities, but Doggett was not as surprised by this since he remembered William was special as a baby. But all this talk...about a virus depopulating the planet was becoming too much.   
  
He smiled and reached for Monica's hand and she took it, clasping it in her own.   
  
Mulder and Scully smiled at one another and Scully absently stroked her belly, feeling the baby stretch and roll beneath her palm.   
  
Shortly before Doggett and Reyes were about to head to their hotel, Scully had insisted on getting a selfie photo with her good friend and promised to text it to her. "You're always welcome to stay here," Scully offered. 

"So you don't have to use all your resources before you decide where to settle," Mulder quickly added.   
  
Doggett and Reyes looked at one another and seemed to consider for a moment. "Thank you, Mulder...Dana," Doggett said. "We might take you up on it. It'll be great to live closer and catch up. It's only been sixteen years."


	17. Chapter 17

**Notes for the Chapter:**

> This will probably be the last chapter before Spooky...gonna leave you with a little cliffhanger. Or if you need plane reading, lmk. Maybe I'll add more.

Later that night, Scully found herself restless. Her growing belly wasn't helping much even though she knew once the tiny life was born it would all be worth it. After the second trip to the restroom so far that night, she settled back into her place on the right side of the bed. Mulder shifted next to her and settled his arm around her waist. Finally, she drifted off to sleep.   
  
Soon enough she saw herself running...through a place she didn't recognize. Fear and anxiety radiated through her, propelling her forward, yet the weight of her midsection had slowed her down.   
  
The next thing she knew, she was face to face with a man she thought to be long dead. The smoking man.   
  
Before she could utter a word of disgust and contempt, the image was replaced by a sick Mulder and several other civilians. The bridge. "No, this doesn't happen." Then she saw William, only he wore an expression she didn't recognize. "Will---Jackson!" Her voice pierced the air, yet was silent in an instant.   
  
A sense of dread settled over her and she closed her eyes, willing it to disappear. 

  
The next thing she knew, she was surrounded by the familiar sight of their bedroom and she was gasping. Looking over, she realized Mulder was still surprisingly asleep and she settled down into the pillows, folding her hands over the baby who shifted inside of her. 

"Did that wake you too, sweetie?" She whispered in an attempt to calm and steady her breathing.

\-----

Scully hadn't been herself lately. Mulder attributed it to William's sudden departure and perhaps the pregnancy hormones. She was almost twenty-five weeks along and the pregnancy was becoming increasingly difficult on her body as it progressed. Back pain, fatigue, and nausea. She mentioned that nausea subsided after just three months with William, but each pregnancy was different. He did whatever she asked, much to her appreciation. Be it a backrub or fetching her the craving of the day. He was there for all of it and he wouldn't have it any other way.   
  
Today, however, she seemed to be in better spirits. It was the fourth of July. In past years, prior to their separation, they would climb on the rooftop and watch fireworks together. That was a no-go this year for obvious reasons. Instead, they sat side by side on the front porch. It was a nice change of pace to have Scully with him. He had spent the past few years alone on this porch.   
  
Mulder smiled as he felt Scully's hand instinctively reach for his.    
Scully's other hand rested on her expanded abdomen. They watched several fireworks in the distance. The view wasn't nearly as good due to the many trees surrounding the property obscuring their view, but they still witnessed a good show. Each firework seemed louder than the last. 

  
Scully gasped suddenly, causing him to look over. 

  
She caught his gaze and smiled. "I think our daughter isn't a fan of the noise," she laughed. "She kicks me each time." Mulder scooted closer to her and placed his hands on her belly. 

"She's part you and part me, Scully. I think we might be in trouble." 

"Maybe," she smiled. "But I wouldn't have it any other way." 

She was right and neither would he. They had been given this wonderful gift, to finally be parents and he wouldn't trade it for the world.   
  
They only hoped that their son was safe somewhere, wherever he was and got a nice view of fireworks.

\----

Mulder woke to the sound of Scully's terror-stricken voice. "Mulder!" "MULDER!" She screamed.   
  
He felt her hand shaking him and he bolted up, instantly alert. "Scully? What is it? What's wrong?!" Despite the darkness of the night, he could see the fear in her eyes as her lips moved to form the words but couldn't.   
  
It was then that he noticed the bed was wet. He wasn't an expert by any means, but he knew it was far too soon for the baby to come. As he pulled back the covers, the reality of the situation hit him like a ton of bricks.    
Blood. Lots of it. Something was terribly wrong. He felt a sickening feeling in the pit of his stomach. No, he had to keep calm, Scully was already losing it. He needed to be strong for her.   
  
He swung himself out of bed and grabbed his phone and with trembling fingers, dialed 911.   
  
Somehow, he managed to finish the call without losing it and he turned to see Scully's crumpled form at the side of the bed. "I--I haven't felt her move at all today. Mulder, I can't feel her...Oh God," she said, shaking. 

  
He was at her side in an instant, drawing her into the warmth of his arms. "It's too soon. I can't lose her, Fox!" She began to sob violently. 

  
Mulder pulled his hand back from the dampness of her pajamas, looking at the bright red blood. He was terrified. 

"We won't lose her," he whispered into her hair, partially to assuage his own fears, but he had to stay strong for her. "We won't. I promise," Mulder kissed her forehead as he forced back his own tears. He couldn't lose either of them, it would kill him.   
  
He pulled back, looking down to see Scully cradling her eerily still abdomen as tears streaked her face. A moment later, he felt Scully go unusually still in his arms. 

"Scully?! Talk to me!" He could no longer hold back the tears. "Stay with me, please!" he shook her gently.   
  
As he cried and waited for help to arrive, he said a silent prayer to whatever God was listening that the love of his life and daughter would be okay.

 


	18. Chapter 18

**Notes for the Chapter:**

> Ok, due to popular demand...here is one last chapter before Spooky. :)

It seemed like an eternity before the ambulance arrived. He had carried her downstairs to make it easier for the EMT to get to her, but with each passing minute, he found himself cursing the gods that he had chosen to live in such a rural area.  
  
He was frantic and the paramedics had asked a barrage of questions. "Please be careful with her," he found himself saying. The logical part of him knew they already knew that. "She's pregnant," he repeated. He couldn't stop himself. He couldn't think straight.

"How far along?" One of them asked. A stretcher was unloaded from the back of the ambulance and he watched as another EMT checked her vitals, noting she was unconscious due to the amount of blood loss. 

"Uh about twenty-five weeks, I think. She just had a checkup recently. Everything looked okay. I don't understand, the doctor said--" He rushed frantically as he watched them secure an oxygen mask over Scully’s face.

"Okay, just calm down, sir."

Mulder wanted to scream. He might lose his wife and his child, how dare anyone tell him to calm down! Again, part of him knew getting upset wouldn't make anything better, so he tried as hard as he could to remain composed.

  
As they loaded her onto the stretcher and into the back of the ambulance, Mulder crawled in after her. He folded his hands and closed his eyes.

"Mul--der," she whispered weakly. 

  
His eyes went wide and he moved to take her hand in his. "Please...you have to save her," she begged. 

  
Mulder looked at her in confusion until he realized what she was asking of him. "If something happens to me, you have to save her," she pleaded.  
  
Mulder shook his head. "I won't lose either of you!" He insisted while he caressed her face.

"Promise me!" She repeated, tears falling from her eyes as she searched his for confirmation.

"Okay, I promise," he said reluctantly. He just hoped and prayed that it wouldn't come to that.

\---

Jackson was once again in hiding. It killed him to have to leave Dana and Mulder so suddenly, but he sensed he was being watched once again. Just when he finally started getting used to the idea of having a normal life. Thus began the hiding in inconspicuous places, crappy motels and living off of food from convenience stores. 

  
It was times like these where he missed being a somewhat normal teenager with a smartphone. It would help kill time, but it would be just another device used to track him. Tonight he sighed as he sat on his motel bed, oddly satisfied by the cup of ramen noodles he just ate. His missed his adoptive mother's home cooking. Dana cooked pretty well too and being with them brought the familiar comforts of home. 

  
Suddenly a sharp pain pierced through his temple and he gasped. He could see his mother, gasping in fear and pain. The baby. Something was wrong. He wasn't sure what, but it wasn't good. Usually, he could sense the baby in some way. Whether it was hearing the thumping of her beating heart or content and distress in the womb. Tonight, he couldn't though. And oddly enough, it scared him.

The connection he had with the tiny life was unexplainable. Maybe it was because part of him always wanted a sibling. She would be the only other one that would understand him in the way that not only ordinary siblings did. Though his DNA had been manipulated, they shared their mother's alien DNA. It was the same DNA that allowed him to share the special connection with Dana. Katherine. Katie. "Kit". That's what they settled on as the baby's name. The fact that she had a name made her even more real, and he couldn't help but be terribly afraid for Dana and his sister that hadn't yet been born.

\---

It felt like an eternity before they arrived at the hospital, but it had only taken twenty minutes. Mulder nearly lost it when he was forced to wait in the waiting room when they wheeled the love of his life away. He sat in the waiting area, resigned, holding his head in his hands. The feeling of powerlessness he felt not too long ago was back in full force. Once again, he couldn't help but find a way to be at fault in this situation. Before they had taken her away, he had screamed at them to save her and the baby. Why couldn't their happiness ever last? 

  
The sound of footsteps startled him and he nearly jumped, hoping it was the doctor. He sighed, seeing Skinner. He nearly forgot the panicked call he’d placed to his former superior. He walked with a slight limp and a cane, but he was otherwise the same old Skinner.  
  
As if sensing his friend's disease, he placed his hand on Mulder's shoulder. "Any word?"

"Not yet," he sighed.  
  
Skinner managed to ease himself next to Mulder with a sigh. He undoubtedly knew what was going through his former agent's head.  
  
They sat in silence for several minutes before the doctor walked out and he was back on his feet instantly. Skinner followed surprisingly quickly as well. "How is she?" He demanded. 

  
The doctor managed a smile. "She had a vaginal hemorrhage, but we managed to stop the bleeding. She and the baby are both just fine."

Mulder released a long breath he hadn't realized he had been holding in. He ran both of his hands through his hair before shoving his hands into his pockets. "I want to see her." The doctor nodded.

"She's still in an out of consciousness, but you can see her."

Mulder looked back at Skinner who nodded. "Go," he urged. "I'll be here." Mulder managed a small smile and nodded before he followed the doctor to the hospital room. 

Inside, Scully was attached to an IV and several wires and monitors. Two were strapped to her abdomen. Scully's eyes were closed and she wore a pained expression. Mulder reached out and clasped her hand, filling it with warmth.

"We will need to monitor her for a while and do more tests since it's such a high-risk pregnancy, but you've got a little fighter in there,” the doctor said.

Sudden unexpected tears filled Mulder's eyes. "Just like her mother," he whispered.

**Notes for the Chapter:**

> Now we can all breathe easy knowing Scully and the baby are okay. I'm making you wait until the next one though. ;)


	19. Chapter 19

**Notes for the Chapter:**

> I'm back and trying to recover from Spooky Empire...and meeting Gillian ;)...hope you guys enjoy this one!

Scully shifted uncomfortably as several voices filled her thoughts followed by taunting images. William, the smoking man, Mulder, Reyes and...Doggett? She couldn't hear the words...couldn't make out what was being said. 

She willed herself to open her eyes and instantly she bolted up into a sitting position on the bed once the voices became too loud to bear. She took several deep breaths as she clasped her forehead in her hands. Suddenly, the sound of monitors filled her thoughts, causing her to open her eyes. 

She winced against the bright light. It took her a moment to realize she was in a hospital room much like the one she was in when she had her first seizure several months ago. 

As she sighed, she became aware of another sound. A fetal heart monitor. Suddenly, the memories of last night came flooding back. She threw back the hospital blanket to see two monitors strapped to her abdomen in addition to the familiar IV in her arm. It took her a moment to get her bearings, but she only had one thought. The baby was okay. 

Blinking back tears of relief, she placed her hand on her abdomen and then eased back onto the pillows of the bed. "You're tenacious aren't you," she whispered with a teary smile. "You really scared us, yes you did," she said as she suddenly felt the baby shift inside. She gently rubbed the spot. After squeezing her eyes shut, Scully turned to see flowers and a card on the table beside her bed. 

Where was Mulder?

\----

Mulder nearly spilled his coffee as he returned to Scully's hospital room as fast as he could. To his surprise, she was awake. As he approached her room, he caught her gaze. It was one that demanded answers immediately. 

"Scully!" He breathed, almost dropping his coffee once again as she began to sit up. 

"Mulder!" He was quick to gently push her back down to the hospital bed. 

"You need to lie down." 

"What happened?!" She demanded, searching his wide green eyes. "The baby--"  

Mulder gently moved to cup her face in his hands as he looked directly into those blue depths.

"She's fine," he said quickly. "You had a hemorrhage and lost a lot of blood. They needed to give you a blood transfusion."

Scully released a slow breath as she sank back into the bed. It was then that she noticed a dull headache and slight dizziness. She closed her eyes, silently thanking God that she and the baby were okay. "Oh God," she teared up.    
  


Mulder took her hand in his, causing her to open her eyes and turn back in his direction. They both regarded the flowers at the same time. 

"You got me flowers, Mulder?" Mulder shook his head. 

"No...I," he began and then reached for the card. He handed it to Scully, figuring it was hers to open first.  _ "Get better soon" _ it read, signed  _ "Love, J". _ Scully's eyes welled with tears and she handed the card to Mulder who was watching her curiously.

Scully rested her hands on the now active swell of her abdomen as she watched Mulder. He looked back at her with tears in his eyes. The genuine concern from their son warmed both of their hearts. Especially since he had left so suddenly. They had been convinced that they had done something wrong or pushed him too soon. "I hope he's okay," Scully whispered.   
  
Mulder set the card by Scully's bedside. He took Scully's hands in his own. "He will come back to us, Scully. I know it." Scully closed her eyes and nodded slowly. 

"When can I get out of here?" She asked. While she was the best doctor, she was also the worst patient.   
  
Mulder sighed. "I'll find the doctor. You stay put," he said.

Just then, the doctor appeared, startling both Mulder and Scully from their thoughts. "Ms. Scully. I'm Dr. Blake. Glad to see you're awake and doing well." 

"Is everything okay with the baby?" Scully asked. 

"You had a vaginal hemorrhage and lost a considerable amount of blood and we had to do a transfusion, but we were able to stop the bleeding. The baby is doing just fine. A little fighter you've got there." Scully turned to Mulder and they shared a teary smile. "We'll need you to stay here for another day or two for observation, but I see no reason to keep you any longer. You will, however, need to stay off your feet as much as possible when you return home. I know you're aware how high risk your pregnancy is and we need to make sure we do everything possible to avoid further complications." 

Scully nodded, relieved that all she had to worry about now was bedrest and not leaving the hospital without her baby alive and well within her.  As much as she knew the risks of this pregnancy, she had grown attached to the tiny life inside of her and she couldn’t bear the idea of losing her. The idea was too much to entertain. The doctor didn't have to tell her what kinds of complications. Premature delivery, stillbirth etc. 

"I'll make sure she stays off her feet," Mulder assured her.


	20. Chapter 20

**Summary for the Chapter:**

> I hope you guys really enjoy this one. I've always enjoyed the wifegate. ;)

Much to both of their relief, Scully had been released from the hospital the following evening. Mulder looked over and smiled at Scully who was absently rubbing her belly as she often did these days. "Is she moving a lot?"

Scully looked over and smiled. "Yes, I was so worried before I had gone to the hospital. I hadn't felt her move all day."

Mulder reached over and placed his hand on her belly and Scully intertwined her fingers with his own.

"This isn't the way home, Mulder," she said suddenly.

"You're right, it isn't," he said, earning himself a raised eyebrow.

"Where are we going?"

"You'll see,” he said wryly.

A few minutes later, Mulder pulled into a shopping plaza, right in front of a Kay Jewelers. 

Scully looked at him skeptically.

"What? Did you think I'd forget?"

Scully sighed in exasperation as Mulder got out and went around to open the door for her. 

They went inside and were greeted immediately by a friendly sales associate.

Mulder informed them that they were just looking around when Scully suddenly stopped in her tracks.

"Mulder."

Mulder turned and saw her looking at a section of white gold diamond rings when his gaze came to rest on a simple white gold band with a diamond accented ribbon that caught her attention.

"This one," she said. "It's perfect." 

Scully had fallen in love with the ring immediately. It was simple, but not boring either. Something that symbolized their enduring love for one another. The design was perfect and it was something she could wear whenever she wasn't in the surgery bay.

"So when is the big day?" The sales associate, the younger man, probably in his early thirties, asked as he glanced at her belly.

Mulder and Scully looked at one another for a moment. It was a question they supposed could have a double meaning considering her pregnancy was clearly visible now. They assumed he meant "wedding date", however.

"Oh um, we've actually been married for almost sixteen years...but we weren't really ring people," Scully explained. It was partially true. Though for a long time, Scully had to keep their marriage a secret while Mulder was still in hiding. A ring would raise more questions amongst people. 

Mulder nodded. It felt good to hear her refer to themselves as a married couple. They never needed a formal piece of paper to commit to one another, but he couldn't help but admit that it felt good for the world to know she was his and he hers.

He looked around more as the jeweler took measurements of Scully's ring finger. It was then that he saw it. A tungsten carbide ring with koa wood embedded in the middle. "Good choice," the sales associate said, catching his attention.

"That is our wood-inlay rings line. Very popular and the koa wood is one of the most expensive woods in the world. Tungsten carbide is a very durable material."

"Oh really?" Mulder said with a smile. "Well, consider it sold then."

Over the following week, Mulder spent most of his time holed up in the nursery, putting together the furniture that arrived a few days ago he had ordered. It was something he had been procrastinating on and he was determined to get it ready this week. 

Scully was already in her 26th week and she and the baby were doing well despite the frequent bathroom trips and challenges getting comfortable enough to sleep at night. She was craving a wide array of things, but her favorite was watermelon. He lost count of how many random trips he made to the store, but he was happy to oblige. This was their second chance and he wanted everything to be perfect for her.

Once the furniture was assembled and the basic decor was finished, he surveyed his handiwork. He’d bought a little stuffed Fox for the baby and set it beside the crib. Mulder briefly considered an alien theme as he thought of the onesies he bought for William but decided it would be best to try something fresh and new for his daughter to be.

He and Scully agreed the baby would sleep in their room for a few months and then they would attempt co-sleeping for a while before transitioning her to the nursery crib.

In addition, he decided to invest in a costly home security system with cameras so they could see and monitor things from their phones. He was determined to do everything possible to ensure the safety of their daughter.

"Mulder?" Came Scully's voice followed by a soft knock on the door.

"I'll be right out," he said quickly. Once he heard Scully's footsteps retreat, he opened the door and closed it quickly behind him.

He wanted the final nursery touches to be a surprise for Scully. "How is it going in there?" Scully asked, bracing her hands on her lower back. 

Mulder smiled as he moved to kiss her. Her belly button had recently popped out and he thought it was adorable how her belly filled out his shirts. He wasn't going to risk telling her that though. Her mood swings had been unpredictable lately. "Good, almost done," he nodded, placing his hands on the sides of her belly.

"She's as big as an eggplant now, Scully," he said, hoping to impress her with the research he'd done.

"Oh, don't remind me," she said, though she was impressed on a day to day basis on everything he was learning. He had read _What To Expect_ that first time around, but it was so many years ago.

"My hands are swelling so much that I can't get my ring on and off without a fight," she frowned.

"You know what's good for that, Scully? Epsom salt," he explained, clearly impressed with all he'd learned. 

She couldn't help but smile in spite of her slight annoyance. "Okay, but I'm starving. I ate that watermelon and now I need a huge burger and fries. Speaking of which, I happened to see a donut burger on a post about the state fair and I can't get it out of my head."

Mulder scrunched up his face. Now that was un-Scully like. "Wow, Scully. I feel my arteries clogging already," he joked as he did a heart constricting motion against his chest. "It can't be good for the baby."

"That wasn't a request Mulder. I need it. Or at least a donut and a burger so I can do it myself."

"Okay, okay," he sighed in defeat.

His phone vibrated just then and he knew it was from Monica. She wanted to plan Scully a surprise baby shower. He knew Scully hated surprises, but this would be a good one, especially since it would be all their close friends and not some random women from her mother's church group, God rest her soul.

They were still needing a lot of essentials like diapers and onesies. Since Scully had told him she was pregnant, he was learning so many new things and the first thing he learned was that there were so many new things to choose from since she had been pregnant with William.

There were dozens of different types of baby carriers, cribs, toys and things like breastfeeding pillows. It was almost as if they were first-time parents again. It had been that long.

As he went to heed Scully's request, he took a peek at his phone to see Monica's guest list included Skinner, Arlene, she and John Doggett and she was asking about Scully's family. Sometimes he felt depressed when thinking about the fact that the baby wouldn't have living relatives on his side. But Scully still had her brothers. That meant telling Bill and Tara though, he thought with a heavy sigh.


	21. Chapter 21

Mulder opened his eyes to see his Scully fast asleep beside him on the couch, both their feet propped up on the coffee table as they often did. Scully had taken to naps while Mulder joked that it was a sign that they were both getting old as he often joined her. Scully however, would always be as beautiful to him as the day she first walked into his office. He still couldn't wrap his mind around the fact that they were in their 50's and were having another baby. Better late than never. They hadn't gotten to be parents to William, so this second chance was a miracle.   
  
The way she laced her fingers over her belly while they napped together on the couch was adorable. He'd often wake before her and watch her sleep until she seemed to sense he was staring and then would open and narrow her eyes at him. "What Mulder?" She asked, trying her best to sound genuinely annoyed while a smile tugged at her lips. 

"Just admiring how beautiful you look and thinking how lucky I am. So sue me." 

She rolled her eyes. "That can't possibly be it, Mulder," she continued. She knew him better than anyone else. 

"Did you tell Bill about the baby?" He asked.   
  
Scully shifted to face him. "Since when do you care about Bill?" 

Mulder stumbled for a response. "Well, I just thought that maybe you would have told him. He is your brother even if he hates my guts." 

Scully sighed. "I honestly haven't talked with him since the funeral. He might still be stationed in Germany, but I'll email him tonight...that might be the easiest icebreaker." In all honesty, she wasn't up to deal with Bill's reaction over the phone or in person. He nearly jumped for joy when he found out about the separation between her and Mulder.   
  
Maybe she would  _ try _ to reach out to Charlie as well. She hadn't seen him in years until the funeral...maybe he was coming around. Her daughter deserved to know what family they had left.

\----

Jackson had tried to stay away. Someone or somebody was after him, but he wasn't sure who. He began to have visions again and he sensed that the smoking bastard who projected himself into his visions was alive. It scared him, terrified him, and part of him wanted to die all over again. 

  
The worst of it was that he felt that Dana and his baby sister might also be in danger. Maybe Mulder too. He wasn't quite sure, but when the smoking man had shot him, he had shot him whilst thinking he was shooting Mulder. What kind of Father shoots his own son? It made him physically sick. He was still getting to know Dana and Mulder, but he was growing closer to them. His adoptive parents died because of him and he didn't want to see anyone else hurt.   
  
So here he was, hiding in the brush, hoping to talk to them. He didn't want to hurt or scare Dana with his visions and to be honest, he was feeling lonely.   
  
Mulder had opened the front door to the patio and that's when Jackson decided to walk out. "Hey," he said.   
  
Mulder jumped at the sound, placing his hand over his chest. "Oh shit! You scared me, kid," he managed a small laugh. 

  
Jackson shrugged. "Sorry," he looked down apologetically. 

"Don't worry about it," Mulder tried to sound as casual as possible.    
An awkward silence passed between them for a moment before Jackson walked up the steps, but not before looking around him.   
  
Mulder could sense something was bothering his son. "Is Dana here?" He asked. 

"She left to go to the hospital," he started. 

  
Jackson's eyes went wide. "Is she okay?"

Mulder smacked himself mentally. "Oh yes. She works at the hospital...well, she's on leave, but she just has to take care of a few things." 

Mulder smiled at the relief in the young man's face. 

"Oh."

"Want to come inside?" Mulder asked, sensing his affliction.

Jackson nodded and followed Mulder inside. "Something to eat or drink?" He asked.   
  
Jackson shook his head as he took a final peek through the window before he found his way to the couch. "No thanks." 

Mulder nodded and sat next to him. He hoped the kid had a decent place to stay and was eating properly. He wanted to laugh at that thought. He was already feeling like a Father.   
  
As Mulder reached for his phone to text Scully, a card on the coffee table caught Jackson's eye. It was a green baby shower invitation that was decorated with a Fox, Rabbit and a Blobfish. He couldn't help but chuckle.   
  
Mulder had texted Scully to come home as soon as she was able, but didn't say why. He wasn't going to risk her getting into an accident while speeding home. 

"She should be home soon," Mulder said as he looked over at Jackson and his gaze went to the card he held in his hand. 

"You know," he started. "If you could come, it would make her really happy." 

Jackson turned towards him in surprise. 

"I mean, only if you want to," he said, hoping he wasn't crossing any lines. 

  
Jackson nodded and turned back towards the card. "When she was pregnant with you, her mom invited all these women from church that she barely knew," he couldn't help but say.   
  
Jackson laughed. "Wow...it kinda sounds like something my adoptive mom might have done. My adoptive parents were pretty religious...they were always really active in the community." 

Mulder nodded. "We don't have a lot of friends or relatives left, but I wanted to do this for her." 

Jackson couldn't help but feel touched by Mulder's obvious affection for his birth mother. Their love for one another seemed to radiate off of them everywhere they went.


	22. Chapter 22

They made some small talk until they heard the sound of a car pulling up out front which was followed by key turning in the front door a few minutes later.

Jackson shoved the baby shower invitation into his pocket for later reference. "Hey, Scully. Look who's here," Mulder said catching her by surprise.

Scully dropped her keys and the files she had been holding to the floor once her eyes rested on Jackson. For a moment, they had taken in the sight of one another even though it had only been a few weeks since they had last seen him.

Jackson's gaze fell to Scully's belly. The baby had gotten bigger.

"Oh…Jackson, um hi," she tried to keep the evident shock from her voice.

"I'm sorry I left so suddenly last time," Jackson said as he stood up, moving forward to help her pick up the things she dropped.

"Don't worry about it," she insisted.

A sense of disease gnawed at her. Jackson obviously had something to tell her, she could feel it. She had felt it since the day he left in such a hurry.

"How is the baby?" he asked, a lame attempt at surface level conversation. He suddenly felt hesitant to say what he knew would be coming next. He wasn't sure how to explain it, but he knew that he had to.

Scully looked up and smiled at him as she placed her hand on the swell of her abdomen. "She's just fine," she said happily. "But everything is starting to hurt now and I have these ridiculous cravings."

Jackson couldn't help but laugh.

Scully wished she could freeze time and savor this moment forever because she sensed what was about to come next.

The baby shifted inside of her, sensing her trepidation. Gently, she ran her hand over her abdomen to comfort not only the life inside of her but also herself.

Mulder motioned for Scully to come and sit next to him. "You came to tell us something," Scully said suddenly.

Mulder was startled by Scully's abrupt tone.

Jackson sighed. While he had gathered some control over the visions these past few weeks, the connection they shared seemed to be unbreakable.  
As he sat back down, he folded his hands in front of him. He had practiced what he would say over and over before he had come over, but it didn't make it any easier.

Sensing Scully's apprehension, Mulder reached over with his right hand and grasped hers into his own, giving her the strength she needed to deal with what lay ahead of them.

The movement didn't go unnoticed by Jackson.

"Honey," Scully found herself saying. She wanted to reach for him but was afraid of pushing him too much. "Tell us what it is."

"I...I didn't want to tell you. It might not be safe. I might be putting all of you in danger."

"You don't have to worry about us," Mulder said.

It didn't have to be spoken for Jackson to know what Mulder meant.  _It's our job to worry about you._ He could hear it in his mother's thoughts and he saw it in her facial expression.  
Love radiated off of both his birth parents, so much that it was almost overwhelming. His adoptive parents loved each other, but this kind of love was unlike anything he had seen or witnessed before.

Jackson stared at a spot on the wooden flooring of the house. "Umm, I think the smoker…the one who calls himself my creator is alive."

Scully gasped, causing him to look up. From the look on her face, he could tell that she may have known this was coming. Her hand slipped from Mulder's and went to rub along her abdomen where their baby rested. The gesture was instinctive as if to protect the small life inside.

"But I killed him," Mulder insisted, slipping his arm around Scully's shoulders and bringing her close.

"I shot him after…" he trailed off, looking over at Scully. He recalled that the bastard had still been standing after several gunshot wounds just before he pushed him into the water. He had been so beside himself that it didn't register at the time. A man with several bullets to the chest shouldn't have still been standing. "Fuck," he whispered.

"Where is he?" Scully asked, her voice laced with fear and rage at the same time. The feelings of being physically violated came back in full force. Everything that they and their son had to endure because of that man. "I will kill that sonofabitch," she said icily.

"You can't," Jackson said suddenly, startling them both. "He already hurt your friends…he," Jackson started, looking over at Mulder. "Wouldn't hesitate to hurt you."

Mulder still had trouble coming to terms with the fact that his own father hadn't hesitated to shoot him, not realizing it was William he had shot. "But maybe not you," he said looking over at Scully.

Suddenly, Scully recalled her vision. The one where they were on the bridge and Mulder had told her that the old man had saved her life. Monica had said the same thing. But why? The man was sick and delusional.

"I gotta go," he said.

"No!" Scully said, jumping to her feet.

"I have to. I'm putting you all at risk by being here." They knew stopping him would be pointless and just like that, they had to let him leave once again. The baby began to kick furiously as if protesting her brother's departure.

He looked back once more at them and managed a small smile as he sensed the innocent presence of the baby. If anything, he had to make sure he kept her safe. Things had to be different for her.


	23. Chapter 23

Scully cried for some time after her son’s departure. They had expected that their son would come and go from their lives, but Scully’s pregnancy hormones were making it exceptionally difficult. The intuitional side of Scully could almost swear if she didn’t know any better her children were communicating, but the rational side of Scully would assume the baby was just reacting to her emotions. 

“Do…do you think he’s alive, Mulder?" she asked as she wiped away her tears. 

  
Mulder knelt in front of her, taking her hands in his. “I…I don’t know, Scully. But I shot him and pushed him into the water. He wasn’t moving.” 

“But clearly, he’s survived worse,” she pressed. 

  
Mulder rubbed her palms with his thumbs before he stood up and kissed her forehead. “You should eat something,” he said finally. 

  
Scully sighed. He was right, she was hungry. “I think I’ll invite Monica and John over…maybe Monica could give us some insight. If he’s alive, she might know where he might be hiding.” 

Mulder nodded. “Okay, give them a call. I’ll make enough for four.”

\-----

An hour later, the four of them sat down to eat dinner which consisted of spaghetti with meatballs and salad. The salad was Scully’s idea of course. “Thanks for having us over Dana,” Reyes said with a smile. “I must admit, I didn’t have much of a social life for quite some time. This is a nice change of pace.” 

“I haven’t gotten out much lately either,” Doggett said. “Even in the city.” 

“Is everything okay with the baby?” Reyes asked. 

  
Scully managed a small smile as she palmed her abdomen under the table. “Yeah, she’s…she’s doing well. Things are starting to hurt, but once she’s here,” Scully said with a hitch. “I think it’ll all be worth it.” Part of her was afraid something would go wrong, whether it be stillbirth or complications during birth. 

  
Once they had finished up, Scully started to stand and collect the dinner plates before Mulder quickly jumped in, followed by Doggett. “We’ll take care of this, you sit down,” Doggett insisted.

  
Scully sighed. Normally, she’d protest, but it would be a good opportunity to talk to Monica about why she asked them to come over. 

  
Of course, Monica seemed to sense something was up. “Dana, as much as I enjoyed dinner, I have a feeling this wasn’t just a social call,” she whispered as she folded her arms, leaning closer to Scully who was seated just opposite her. 

  
Thank goodness they had invested in a table that sat six. Their old table for two wouldn’t work well with a baby anyways.   
  


Scully told her about William, about his visits and about what he had come to say about the smoking man. “Is there a chance he could be alive, Monica?” she whispered. 

  
They could overhear the guys talking in the kitchen. Reyes pulled back just slightly and sighed. 

“He does have access to alien DNA. The same DNA that you have and that he had given me when he sought me out all those years ago, I saw a man that should have died but didn’t. It defied all logical explanation.”

"Monica, you....you said he gave you the same DNA," Scully said. She motioned for her friend to turn around. "I'd like to see your neck," she prompted.   
  
Monica did as she was told and Scully gingerly brushed her hair aside. Sure enough, a small scar that indicated incision was there.    


Scully gasped and Monica looked over. "What is it?" 

Scully sighed. "I know you read quite a bit of our work. Do you remember my abduction? I have a chip that caused cancer with it's removal. But Mulder's abduction was different, he doesn't have one." Monica turned to her in shock. "An implant," Scully continued. 

"But I don't have any symptoms of lost time." 

"You wouldn't need to. As you know, the smoking man violated me over one night. And did something that allowed me to become pregnant with William. It wouldn't take long for a simple implant." Scully retrieved a hand mirror to show her friend.    
  


Monica looked back in shock. "But why?" 

"To control you. To know everything about what you're doing and where you are at all times. And maybe to even, make you pregnant."

"Dana...I'm 50. That ship has sailed..." she stopped as she realized what she was saying. "In fact, I'm close to menopause." 

Scully folded her arms and raised an eyebrow. "Monica, I'm 54...I'm supposed to be infertile and here we are." She couldn't help but smile. Scully continued. "You're slightly younger and assuming your ova remained intact all these years, it's not outside the realm of possibility. There's Janet Jackson..." 

Monica considered for a moment. She never understood why the smoking man came to her of all people. "Well, now that you mention it, the smoking man did try to launch another project after Crossroads years ago. I mean, if alien DNA can protect us against common illnesses and diseases, what else could it do?" Scully took a deep breath as Monica continued. "I don't know the details, but his interest was in women past childbearing age. If perhaps alien DNA can give us immunity, perhaps it could rewind the biological clock that is inside of all of us. Dana, your ova were taken from you...the same goes for all women abductees. I think, in a way, the smoking man wanted to give back something that was taken from you." 

Scully stiffened. "What are you saying, Monica?" 

"I'm saying alien DNA may have made it possible for you to conceive again. As a result, your child would share this DNA. But that project was shut down within months, there is no way to know for sure."

After Doggett and Reyes had left, Scully couldn't shake the sudden onset of sickness causing her stomach to churn that had come over her. How she was able to conceive at 54 years old while being barren was something that had been on her mind? It was impossible, but the conception date was not. When she found out she was pregnant and how far along she was, there was no question about how the child was conceived or who her father was.   
  
The knowledge that Reyes had been manipulated just like she was was disconcerting. She palmed her abdomen as she felt the baby kick as if sensing her inner turmoil.    
  


Scully stopped by the nursery on the way up the stairs, which was now nearly complete. The windmill snowglobe rested on a shelf opposite their baby's crib, next to where the changing station would be. "Scully?" Scully nearly jumped at the sound of Mulder's voice in the doorway and the globe nearly fell from her hands.   
  
Clutching it tightly, she turned towards him. "Are you coming to bed?" He asked, concern evident in his eyes. 

"Yeah, I'll be there in a few minutes." 

"Everything okay?" Mulder asked as he reached out towards her.

Scully nodded quickly. "Yeah...I'm okay." After Mulder turned and headed towards their bedroom, Scully clutched the globe to her chest and gasped as several images flashed before her eyes.

 


	24. Chapter 24

The following morning, Mulder woke, startled to see the empty space beside him. He saw the master bathroom was empty and the house was eerily silent. Making his way downstairs, he saw no signs of life in the living room. He went back upstairs to retrieve his phone and saw he had a message notification.   
  
He sighed with relief when he saw it was from Scully. _ "I didn't want to wake you, but I have something I need to take care of at the hospital. Be back soon. S." _ He should have felt relieved, but he felt something was off and he had felt it since Doggett and Reyes' visit last night.  

Scully was sure the place she saw in her vision was back in Norfolk. The place looked so similar to the Sugar Factory back at the harbor.   
  
All she knew was that she had to find William. She had to find out whom or what he was still afraid of. Who could still be after him? She thought back to what Reyes had said about the various projects. Mulder had killed Mr. Y and the Smoking Man. Was it possible there were still others who wanted William's DNA? She didn't want to admit it, but it was probable that they had others to step up in their place.   
  
The baby shifted inside of her in protest. She ran her free hand over her abdomen to soothe the baby, all the while hoping she wasn't putting them both into grave danger. "It's gonna be okay," she whispered, fully aware the words were meant more for herself.   
  
Lately, she couldn't get her mother's words out of her mind. "My son is named William too." Somehow she had pushed them to the furthest reach of her mind. Especially when William asked them to let him go.   
  
But her mother's words began to haunt her, reminding her that William was still her responsibly even though she wasn't able to raise him. She had given birth to him and had a responsibly to make sure he was okay.   
  
She debated texting Monica so someone knew her whereabouts, but she thought better of it...especially when she knew Mulder would likely go to them.

\-----

As Scully neared Norfolk, a sign for Chesapeake Bay jogged her memory. She remembered seeing the sign in her vision. She turned, quickly cutting another driver off in the process. She sighed as she heard the blaring of the horn, mentally kicking herself.   
  
It was then that she was reminded of the growing weight resting right on her bladder, which was screaming for relief.   
  
Thankfully, she spotted a sign for a McDonalds a few miles up and stopped for relief before continuing the last leg of her journey.   
  
She watched as a long stretch of river and trees came into view and spotted a rather old, decrepit building on the opposite side of the road. Scully pulled over next to the grassy entrance marked "private property". This was the place she saw. It had to be. 

  
The baby seemed to settle down some, for which she was grateful. Normally, she reveled in the movement, each kick reminding her that she was growing strong and healthy. Today, however, their daughter's insistence on making her presence known added to the guilt she felt about lying to Mulder. She had to keep them both safe and free from harm. But she had to make sure her firstborn was okay too.

Once she exited the car, Scully pulled out her phone and powered it off before sticking it into the glove compartment as she pulled out a flashlight. She patted her hip to ensure her gun was there before buttoning up the front of her coat, which in the coming weeks would no longer be feasible. After glancing around the lonely street a few times, she slipped around the gate and pushed past the weeds that blocked the pathway. It was just a short walk down to the old building that carried no signs of life. 

  
Suddenly a pain seized her temple and she gasped, dropping her flashlight in the process. She could see William running and then the butt of a cigarette. A moment later, the images passed and she took several deep breaths before she reached down for her flashlight and pressed on towards the building. 

  
As she moved her hand towards the door, the movement involuntarily pushed the door open to reveal the dark interior. Scully turned on her flashlight as she moved forward. "Will-JACKSON?"


	25. Chapter 25

Suddenly, a movement to the left startled Scully, causing her to jump. Gasping, she moved her flashlight in the direction of the noise.   
She sighed with relief when she saw it was Jackson. "Oh...Jackson," she wasn't sure if she'd ever get used to calling him that.

"How did you find me..." He started. "Oh, right..." he said, forgetting the answer was fairly obvious. "You shouldn't be here," he said with concern.

"You're running from something. From what? You're safe now...right?" Jackson hesitated and Scully could tell he was holding something back. "Honey," she started, moving closer. "Tell me what it is."

Jackson was startled by her words, how familiar they were and her sincerity. He wanted so much to open up to her, to let his feelings pour out, to allow her to shoulder his burden even if it was for such a brief amount of time.  
  
Scully reached out to touch him and he flinched slightly. "I know you sent me those visions for a reason." It was true, but at the same time, he didn't want to put her or his sister's life in danger. His sister.

Looking down at his birth mother's abdomen, which she unsuccessfully tried to conceal, reminded him of why he was doing this. The connection to that tiny life inside was unlike anything he ever experienced other than the connection he shared with their mother. "I'm sorry. I can't. You should go. It's not safe for either of you here."

Scully took several deep breaths, trying to understand. "Tell me why?" She pleaded.  
  
Jackson opened his mouth to respond when the door to the entrance slammed shut, startling them both.  
  
Panicking, they both turned and ran towards the door, pushing and turning the knob to no avail. "Shit," Jackson muttered as a felt a sinking feeling in his gut.  
  
Scully slammed her hands against it in frustration. "Dammit!" The sound of footsteps approaching made them turn around. Scully shined her flashlight into the darkness with one hand and reached for her gun with the other. "Stop, I'm armed!" She demanded.  
  
She was awarded sinister laughter. "Oh, Agent Scully, you'll come to find that won't work on me." The familiar voice was one she could never forget and she already felt her blood boiling in her veins as the smoking man stepped into view.  
  
He smiled. "Oh, it's so good to see you both. You have no idea how much I want a cigarette, but I know second-hand smoke wouldn't be good for the baby."

\-----

Scully seemed to be taking quite some time with her hospital errand. Mulder sighed. Maybe she stopped somewhere else? The grocery store? To see Skinner possibly? Maybe even Doggett and Reyes?

  
Mulder had woken up feeling a bit under the weather and fatigue seemed to be gnawing at him to return to bed. So much so, that he had barely gotten through his morning run. 

  
He had sent a text to Scully about an hour ago and she still hadn't responded. It had been over four hours since he had woken to her note she had left for him. Ever since the X-Files had been closed and the scare with the baby, she generally wasn't away for more than two hours or so. Shopping was usually something they did together so he could do all the lifting, and she would tell him if she had an appointment to check on the baby. He insisted on being there for all of it.  
  
He began to worry. Did something happen? Was something wrong with the baby? Surely, someone would have notified him, right? 

  
Worry prompted him to dial her number, hoping he didn't seem like an overbearing husband in the process. Before he could fathom an explanation, the call went straight to voicemail, which either meant she sidebared his call right away or her phone was dead or off. Neither of those scenarios sat well with him. 

  
He coughed and then remembered that both of them had Find-My-Phone apps on their computers. If Scully was in real trouble, she would forgive his little trespass later, he thought as he went to find her laptop...hoping it wasn't with her.


	26. Chapter 26

**Notes for the Chapter:**

> Here's one last chapter before Thanksgiving! I hope you guys enjoy it. :)

"Don't come any closer, you black lunged sonofabitch!" A fury unlike any other swept over Scully. Everything that this sick bastard had done to them over the years hit her at full force. 

"If you must know, my name is Carl. I know how you must loathe me, Dana, but you see those feelings are unfounded. I'm the reason you have a perfectly healthy teenage son standing next to you...the reason you are carrying another child so late in life." 

"You're a liar." A mixture of emotions bubbled up inside of Scully and she fought to keep them at bay. For her son's sake, if anything. She thought back to what Skinner had said to her a few months ago. Jackson couldn't hear any of this. 

"Enough!" Jackson screamed, raising his arms in furious concentration.   
  
CSM held his hand up. "I wouldn't do that if I were you, boy...it won't work anyways. I've died four times already. What makes you think it'll work this time?" 

Jackson glared, but as he turned towards Scully, he felt his resolve soften slightly. He recalled the look on Mulder's face when he killed those people at the motel. And now looking at his birth mother, knowing the enduring love she carried for him that knew no bounds, he knew he couldn't bear seeing that same look on her face too. He lowered his arms.   
  
CSM sneered. "I know everything. You and my son were trying to conceive all those years ago. I just wanted to give you back something you thought you'd lost."

Scully steeled herself against his words. She placed a hand on Jackson's arm, while the other came to rest protectively on her abdomen. The need to protect both her children was strong. Not wanting to hear any of it, but at the same time not being able to help herself. "During that time, I was able to gather the samples I needed in order to create a viable embryo." 

Scully drew in a breath at the memory. The lack of agency. The mourning of something she never realized she had wanted until it was forcibly taken from her. "It didn't take." The words taunted her as if it were yesterday. 

"That's what I told them to tell you. I took yours and Mulder’s samples and used them to create the perfect alien-human hybrid."

Jackson was stunned as the realization hit him. "All this time, you sent me those visions. Made me believe that YOU were my father," he growled, clenching his fists. It was, however, a relief that this sick man wasn't his father. 

"I am your creator, Jackson and we still share ties, I am your grandfather. I made it possible for your mother and father to have the child they dreamed of, but they abandoned you."

Hearing the words, even while knowing they weren't true, was like a knife in Scully's chest. As a result of the pregnancy hormones, she felt a lump grow in her throat and tears well in her eyes. But before she could get the words out, Jackson interjected. "THAT'S BULLSHIT! YOU KNOW NOTHING!" He screamed.

The smoking man chuckled. "Dana, as you already know, you have alien DNA and a chip that cured your cancer. It was our hope that the implant in conjunction with the alien DNA would allow women to conceive well beyond the average reproductive window. Men can be Fathers at almost any age after puberty, why not women as well? All I had to do was activate it,” he mused.   
  
Scully shook her head. Seeing this sick, pathetic human being after all these years after surviving a missile strike was unreal. She had seen him in her visions, known he was alive, but she was still struggling with the reality of it. "You think you can play God?"

"Play God...I am doing God's work. I made it possible for you to have this second chance. You should be thanking me. You and Fox," he said, gesturing to her belly. 

"How...how did you know about my baby?" She asked icily. 

"Dana, I know where you are at all times. I know everything about you. Even when you and Fox played house all those years, thinking you both were safe. The FBI sought his help all those years ago with my recommendation. I sent them to you to find him." 

Scully always thought it was odd that the FBI sought Mulder out on such a simple case. 

"It's because of me he's no longer a criminal, but my boy continues to get himself in trouble." 

"Go to Hell." 

"I've been there and back, but boy do I need a cigarette. Thank you for the visit," he said as he snapped his fingers. 

  
Suddenly two men emerged from the shadows, grabbing them both roughly from behind. Before they could react, a cuff was thrown onto Jackson's right hand and then onto his mother's left. "Shit! Jackson yelled. 

"No!" Scully screamed. "You bastard! I will kill you!" 

"If you're both good, you can stay together and we can have a little family reunion," CSM continued.   
  
As they both struggled, they were unaware of the needles that were produced and pressed into their arms. Everything around them slowly became distorted and blurry before fading into black.

**Notes for the Chapter:**

> In this chapter I try to make sense of how William came to be along with baby #2, I hope you guys like my take on it and it's the headcanon that makes the most sense to me. Scully definitely would have done every single test available to ensure William was theirs, there's no way she didn't.


	27. Chapter 27

Hours seemed to bleed into the night as Mulder grew worried and anxious. Scully still hadn't answered his calls or texts and the Find-My-Phone app was useless as the signal couldn't be located. Which meant her phone was either dead or shut off. He called Our Lady of Sorrows and she was not in her office nor had any of her colleagues seen her.   
  
He felt tired, fatigued, and a little feverish as well. It was a struggle to keep his eyes open. If it weren't for the fact that Skinner was no longer at the FBI, he would have been the first person he called for help.   
  
Mulder began to pace the living area restlessly. His body desperately craving sleep while his mind was unable to rest. 

  
The sound of his ringtone caused him to jump, startling him from his thoughts. He raced to grab the phone and his heart sank slightly when he saw it was Monica Reyes, but then he felt hopeful. Maybe Scully was with her and just lost track of time. "Mulder," he said. 

"Age...Mulder," she corrected herself. 

"Is Scully with you, Monica?!" He almost screamed at the receiver.   
  
Monica immediately sensed something was wrong. "Um no, I was just calling to talk about the shower plans and the guest list..." 

Mulder took a deep breath to steady himself. 

"What's wrong?" She pressed on. 

"Scully left early this morning. I haven't heard from her since. Her phone is off and she was supposed to be going to her hospital, but no one has seen her."

\---

Scully shuddered as the images plagued her mind. Running through the hospital, people dying, sick patients, the spaceship...and Mulder. Mulder was also very sick. She had these visions before though. It was supposed to be over, they had stopped it, hadn't they?   
  
A sudden movement from her womb caused Scully to jolt upright and her eyes flew open to a dimly lit room. It was then that she realized she was having a dream and the baby had chosen that moment to make its presence known...as if trying to wake her.   
  
As she moved her hand to pacify the movement, she saw the silver handcuff bound to her right wrist and her memory came rushing back to her. The Smoking Man...and others that attacked them. They were injected with something. But what? She felt terror grip at her, hoping that whatever was in the sedative wouldn't hurt the baby. She'd kill that man with her bare hands.

"She's fine, don't worry," came the familiar and comforting sound of Jackson's voice beside her. She turned, just then realizing that their hands were cuffed together. It made sense. It would make escape more difficult, especially in her current condition. 

"Jackson," she sighed, turning towards him. "Are you okay?" 

Sitting up beside her, he nodded. "My head hurts," he said, rubbing his temple. 

  
Scully reached over with her free hand to examine him and to her relief, he didn't pull away. "Everyone is in trouble," he said suddenly. It took her a moment to realize he was referring to the vision that she hoped was just a bad dream. 

  
Scully's heart pounded against her chest at the realization. Mulder.

 

"Mulder..."

 


	28. Chapter 28

Mulder was startled awake by a knock at the door. While jumping to his feet, he nearly fell over as a wave of nausea settled over him. It took all his strength to force himself towards the door. 

"Mulder? It's me, Monica Reyes." Monica took a deep breath as the door swung open, but she was unprepared for the sight in front of her. Mulder's face was covered in beaded sweat and his shirt was nearly soaking. He looked sick. He was fighting to stand upright. 

"Mulder? Are you okay?" "Just a little feverish. Where's Doggett? We need to find Scully. I'd call Skinner...but he hasn't fully recovered yet," Mulder said as left the door open as he retreated inside.   
  
Monica didn't argue as she followed him inside, shutting the door behind her. "John wasn't feeling well either," she told him. Suddenly, she felt uneasy. 

"Found something. The NSA is able to trace phones that are off, but not necessarily dead. So either someone took her phone or she shut it off. The last traceable signal came from Norfolk, VA." It was where the smoking man sent her to find William, she recalled. Monica nodded in understanding. 

"You think this has to do with your son," she stated. 

"I don't know what else it could be. He told us he thought my black lunged sonofabitch of a father was still alive," Mulder fought to keep his eyes open.   
  
Monica opened her mouth but struggled to find words. Despite his fatigue, Mulder grew suspicious with her silence. "He can't be alive...right, Agent Reyes? Answer me."

\---

Scully began to hum  _ "Jeremiah Was A Bullfrog" _ softly as she clutched her belly with her free hand. Her other was cuffed to Jackson’s left, who was right beside her.

  
The room was minimally decorated and it appeared to be a cellar of some sort with the piping that came up and out through the worn wooden walls beside them. She scoured the room in search of a way out as the baby's weight began to press on her bladder. It wouldn't be long before it started screaming for relief. 

  
Glancing to her side, she noted that Jackson's eyes had slipped closed once again.  _ "Joy to the world, all the boys and girls," _ she hummed in her monotone voice.  _ "Joy to the fishes in the deep blue sea...joy to you and me."  _

"I know that song," Jackson said suddenly, causing her to jump slightly in embarrassment. 

  
Gasping, she turned to him. "Oh God, you heard that? Sorry, I didn’t realize you were awake. I can't carry a tune, but--" 

"The baby likes it," he said suddenly as a grin tugged at his lips.   
  
Scully couldn't help but smile in return. "Yeah. She's usually not so active, but sometimes it's the only thing that gets her to settle down these days. I used to sing it to you too, as a baby. You were the same way." 

Jackson nodded. "I can't explain it but, whenever I've heard that song, it seemed so familiar. Like a memory, I couldn't quite place." 

Scully smiled, not questioning how he could have such a memory. She moved closer to him and to her surprise, he didn't flinch or move away. Instead, he moved closer to her.   
  
The sound of footsteps nearby startled them both, which was followed by the sound of a key in the door and the turning of a lock several feet away.

 


	29. Chapter 29

**Notes for the Chapter:**

> Special thanks to RationalCashew and MonikaFileFan for helping beta these!!!

Both Jackson and Scully struggled to a standing position, moving closer to one another despite their joined hands. 

The door opened to reveal a tall, heavy-set man that appeared to be in his late thirties. In his hands were two trays of food. 

The gurgle in Scully's stomach reminded her that she hadn't eaten in hours, but the weight on her bladder was equally as demanding. "I've been sent to give you food," he said gruffly and to the point. 

Scully hesitated, peering around him as he set the food on a desk nearby. He seemed to be alone. "I need to use the bathroom," Scully said suddenly. 

Jackson looked over at her as if trying to decipher her motives. "Dana?" he whispered.   
  
The man grumbled and looked at both of them suspiciously. "I have been ordered to keep you in this room."

Scully looked at Jackson in a way that she hoped he could sense that her intentions meant, 'trust me'. "I'm pregnant," she said, placing her hand on her abdomen for emphasis as if it wasn't already obvious. "I don't know how much longer I can hold it. I don't want to have an accident and ruin your floors," she said sarcastically.

"Ewww," Jackson recoiled. He seemed to be following her lead. "Please," Jackson insisted. "Just let her go. I don't want to see or smell that. Gross.”

"I know you're pregnant. I'm not stupid," the guard said. Thankfully, he seemed to be reaching for his keys before producing one and reaching for the cuffs. 

As it fell off, Scully rubbed her wrist, which was sore from the metal and before Jackson could make a move, the guard clipped the cuff to a pipe behind them. 

"Move," he said suddenly, pushing her forward. 

"You had better be quick and no funny business if you value the life of that child inside of you."

\------

Monica sighed as she sat next to Mulder on the couch. "That man had access to a toxin that could ensure the death of humanity as we knew it. He also had an antidote...powerful alien biology that is in both mine and Dana's DNA along with your son's. Only your son lacks any human frailties. The smoking man's access to alien biology essentially regenerated him after that missile attack in Roswell." 

Mulder squeezed his eyes shut, fighting fatigue and dizziness. "Why didn't you tell us sooner, Agent Reyes?" 

Monica swallowed. "I too had reason to believe he was dead. And without William, he is unable to act on his plans." 

_ 'I saw it, you're dying, Mulder. The smoking man, he's responsible for all of this'. _ At the time, he didn't believe Scully because she had just had a seizure and wasn't herself. But what if it were true?   
  
As Reyes waited for him to respond, he moved towards the TV and picked up the remote to turn it on. Sure enough, there was Tad O'Malley, the arrogant Republican conspiracy theorist talking about a sudden epidemic leading to thousands of individuals being hospitalized overnight.   
  
Reyes turned towards the TV as he looked back at her. It was impossible, had he gotten ahold of William? "That's impossible," she whispered.

\-----

Once Scully had relieved herself, she heard a sharp rap on the door. "HURRY UP!" The man outside bellowed in annoyance. 

"Ahhh, I'm going to be sick...you don't want me to vomit all over do you?" she huffed, trying to buy herself more time as she scoured the bathroom for some type of weapon and a way out. There was a small window above the shower, but getting out would be a challenge in her condition. 

She proceeded to make some vomiting noises and flushed the toilet once more. "Oh, what the hell?! Seriously?!!" he yelled, grunting.  
  
As she moved towards the window, she sighed in defeat. She couldn't leave Jackson behind. Not after coming all this way to help him.  
  
As if sensing her thoughts, she heard something crash outside down the hall, something that startled the man enough to send him down the hall in the direction of the sound. "Hey!"


	30. Chapter 30

**Notes for the Chapter:**

> Special thanks to RationalCashew and MonikaFileFan for helping beta these!!!

Whatever injection they had given to subdue him had started to wear off. As the guard stomped down the hall with his birth mother, he began to focus hard on the metal of the cuffs around his wrist. Due to the injection diminishing his powers, he had only been able to bend them. He couldn't break them within a split second as he otherwise would.  
  
Dana's anxiety and worry, for both him and the baby permeated throughout his mind. As he stood up, he peered out of the room and happened to make eye contact with the guard down the hall.  
  
Before the guard could react, Jackson spotted a bucket off to the left and sent it sailing forward with a surge of power from his mind.

"Hey!"

Moving towards the door, he dodged around the corner and down the opposite hallway. His powers were not yet 100%, so he didn't want to take a chance in attacking the man with Dana in close reach. Instead, his hope was that the man would follow him while giving his mother enough time to escape. _'Get out,'_ he thought. _'Don't worry about me. I'll be okay, I'll get out. Hurry.'_

\-------

Both Reyes and Mulder had been so overwhelmed by the mass panic displayed on the media that they jumped when a knock sounded at the door.  
  
Reyes looked at Mulder who jumped to his feet and reached for his gun. She reached out to stop him. "Wait! Let me answer it," she insisted.

  
Her gut told her that whoever was at the door didn't wish them harm. She just knew it. Mulder watched her skeptically as she reached for the door while keeping a hand on her gun. Peering through, she sighed with relief and pulled open the door. "Oh, John!" Monica embraced him.  
  
Mulder relaxed at the sight of John Doggett, whose physical state bore a similar resemblance to himself.  
  
Monica pulled back slightly to examine him. He was fatigued and sweat beaded his brow.

"Monica...there's a mass panic about some virus...I don't understand. I knew I had to get to you. You haven't been answering your phone. Someone explain what's going on.” John took a deep breath to steady himself.

Mulder sighed wearily. "I'm afraid time is something we don't have. Scully is in danger as well as our son."

Monica looked between the two sick men. They didn't have a lot of time.  
  
Doggett looked from Mulder back to Monica. "You're not sick."

Monica nodded in confirmation. "I'll explain in the car. We need to go, even though a hospital is where you both should be right now."

"I'm not resting until I find Scully," Mulder said in a tone that indicated there wouldn't be an argument.

\-------

Scully peered out of the bathroom as she heard the man run down the hall. She was torn about trying to escape without Jackson. There was no way she could leave him behind.

  
A dull ache settled in her temple as she felt Jackson calling to her, telling her to get out; that she and the baby would be at risk if she didn't.

  
Before she could open her eyes, she saw Mulder, a visibly sick Mulder along with Monica and John, who was also in bad shape. She saw it in her vision and could feel it. They didn't have much time, but she knew they were coming for her. Then she saw the brush where she left her car and Jackson.  
  
She opened her eyes and sighed heavily before she raced down the corridor in the opposite direction in search of an exit. Her arm curled around her midsection to support the weight of the baby as her gravity had long since shifted. Scully kept turning around to ensure no one had followed before she found a door that led into the brush outside- unsure of how much time had passed. She had guessed that they were approaching wee morning hours.  
  
As she pushed open the door, she prayed no alarms were set off as she pushed into the darkness outside, hoping she'd find her way back to the car and that Jackson would soon follow.

\----

Once Jackson was sure Scully had escaped the building, he came to an immediate halt and the man lunged for him. He lifted his arms and his intent wasn't to kill the man, but stun him for long enough so he could escape.

There was enough blood on his hands and he didn't want to kill unless he had to. He started to feel his powers ebbing back and it only took a moment of concentration for him to send the man sailing down the hall. He landed with a painful grunt as Jackson continued on his way.

It wasn't long after when the sound of alarms filled the building. Dana had made it outside, that much he knew. He began to panic just as he reached an emergency exit. It really was no use. Someone had already tripped the alarms anyway. Fuck!  
  
Just as he pushed open the door, the sound of footsteps filled the hall and he sprinted through the shrubs and thicket, hoping and praying they'd both make it out safely.  
  
What he didn't anticipate was the smell of cigarette smoke and the voice that followed it. "Leaving so soon?"


	31. Chapter 31

**Notes for the Chapter:**

> Decided to add a few more chapters before leaving for Christmas! Enjoy and Merry Christmas everyone!!

"Leaving without saying goodbye?" The Smoking Man mused.   
  
Jackson turned to see the man he hated sitting as he casually puffed on a cigarette.    
He knew if he didn't move soon, he wouldn't make it out. "I bet you have questions, my boy. Why don't you give me the opportunity to answer them?"

It was a distraction, he knew it. He raised his hands in concentration. 

"You can kill me, but just know that I've died many times before and here we are. I already planted the seeds of mankind's destruction," he said as he took a drag of his cigarette.   
  
Jackson narrowed his eyes. "It needs to end somewhere. It's because of you that my parents are dead and you're going to pay for that along with everything else you've done!" Jackson concentrated hard and in a matter of seconds, a loud popping sound ensued, followed by the sound of splattering bodily anatomy and fluids. 

  
He could hear footsteps fast approaching and he took a hard look at the mess of bloody matter on the ground. "That was for my parents...all of them," he said before he sprinted into the trees.

 

\--------

 

Monica, Mulder, and John had been on the road the past few hours tracing the last signal Scully's phone had emitted, though just barely with the mass panic and failing infrastructures. 

"There!" Mulder said, spotting Scully's SUV. 

  
Monica quickly pulled off to the side of the road and Mulder was out of the car before she came to a complete stop. Doggett was right on her heels as they scoured the area.   
  
Scully's car was completely empty of course. "It's here," Monica said. "This is where he started the New Crossroads, a place he thought he could keep his work private." 

"SCULLAAY!" Mulder screamed.   
  
John looked around as he followed close behind. Every step took all the strength he had to keep going. "AGENT SCULLY...DANA!" He forced his vocal cords to cooperate.   
  
Monica stopped momentarily and turned towards him. "John...you should stay." 

"Not a chance. We're finding her and then putting that sorry sonofabitch out of his misery." Monica sighed and opened her mouth to protest. 

"SCULLY!" Mulder tried again as he continued breathlessly. 

  
Monica and John hurried towards him and sure enough, they heard it. "MULDER!"

Mulder's knees weakened at sight of Scully pushing against the branches of trees. 

"William....William is here," she yelled upon seeing them. "He's right behind me, I know it. I think he killed the Smoking Man." 

Relief was evident in Scully's face as she rushed towards Mulder, allowing herself to be pulled into the warmth of his embrace before she started sobbing.   
  
Monica and John shared a glance before they continued forward, allowing the two some space. Mulder pulled Scully in towards him, relishing in the feel of their child between them, warm and safe inside her mother's womb.   
  
Rubbing circles on her back he whispered, "what have I told you about going into dangerous situations without backup?" 

Scully couldn't help but laugh into his chest. A moment later, she pulled back slightly. Her lips curved into a frown as she noticed the evident fatigue in Mulder's features. 

"Mulder you're sick, Oh God...William...this was my vision. William can help, I need to make the vaccine," she frantically stumbled over her words.   
  
Mulder shook his head. "Shh, it's okay, I'm not going to expire right this second, Scully." That earned him a small smile.   
  
As Mulder reached his right hand towards Scully's belly, she met him halfway, guiding it to where the baby was - much as she had done when she told him she was pregnant. 

"The baby...she's okay....that bastard, he didn't hurt either of you? Or William?" He asked as he felt a kick beneath his palm. 

"She's just fine," Scully assured him. "And William...oh Mulder, he's amazing. It's phenomenal...he's connected to her."

"Agent Scully...Dana!"

Scully turned as she and Mulder moved towards the voice. 

Reyes and Doggett emerged with Jackson right behind them.

"Oh God," Scully whispered upon seeing her son again. Without a care in the world for personal space, she rushed towards him and threw her arms around him. "You're okay!"

Jackson, though surprised at the sudden movement, did not pull away and Mulder smiled as he watched their son hug her back.

"I'm fine," he assured, earning a laugh from all four of them. "I'm glad you got away when you could."

Scully pulled away slightly to look him over. "It was all thanks to you."

"I had to kill him," he said. 

Mulder moved towards them, growing weaker by the moment. "You did what you had to protect Scully and yourself."

Jackson nodded, looking Mulder up and down. "You need my help," he said simply.

"I hate to break this up," Monica interjected suddenly. "But there are others and we need to get back into that facility in order to put a stop to what he's unleashed."

"She's right," Scully said. "And I know how," she said, turning to Monica. "I'll need your help, Monica. We can help Mulder and John at the same time."

Monica nodded as she turned towards John. He was drenched in sweat and his skin was warm. He had a fever.  

"I still don't understand what's happening," he said, "but we need to put a stop to it."

"I have the guards handled," Jackson said. "I've been able to map a few points of entry, I will go back the way I came, but the rest of you," he started, pointing to a darkened pathway behind Scully's car. "The rest of you go that way, the trail will lead to the back of the building. They've followed us, so they won't know where to look if you go now."

Mulder and Scully exchanged a brief look, hesitating. "Okay," Scully said, but when it's safe, I want you to come and find us."

Jackson nodded. "You'll know where I am," he shrugged before taking off into the brush.

The four of them bounded town the trail Jackson instructed to them. In the distance, they could hear voices growing closer until they could no longer be heard.

Monica led the way, followed by John, and then Scully with Mulder right behind. 

Scully let out a gasp as she stumbled slightly and Mulder was on it, reaching out to steady her despite his growing fever and fatigue."You okay, Scully?" He whispered, slowing his pace and gently pulling her closer to him.

"My head," she whispered. "It's William."

"Is he okay?"

She sighed. "He's got this...he's already disarmed several of them, not killing anyone but disabling anyone in the way so we can get inside. There is a lab," she groaned, touching her forehead. 

"I can make the vaccine and help you and Doggett, but when we leave we'll need to get the vaccine replicated quickly at the hospitals, we don't have too much time."

The skies grew lighter as signs of dawn broke through and fifteen minutes later, they reached what appeared to be an alternate entrance - a single door behind the vast darkened building but it was coded. As if on cue, there was a clicking sound followed by a blinking green light. William.

Monica reached for the door, glancing back at the three of them before pulling it open. "I've never been to this facility, but he had a few. This very building holds alien science that is the key to immortality that so many seek, yet it also holds the key to mankind's destruction."


	32. Chapter 32

After fifteen minutes of scouring the premises, the coast seemed to be clear with the help of Jackson. Monica suspected that the building likely had a limited number of inhabitants aside from whomever CSM had employed to do his bidding. 

She stopped in front of a door marked "Crossroads" and turned towards the others. Mulder exchanged a look with Scully before turning towards her. "I thought Project Crossroads was long gone."

"It is, but it didn't stop the experiments. There were some things I wasn't privy to...details of experiments and locations of some of these facilities where they were performed were some of those things. I suspect that CSM occasionally questioned my loyalties," she explained as she pushed open the door.

As soon as they entered, they noticed several bodies in lab coats sprawled out on the tiled floor in a  brightly lit fluorescent room full of medical equipment.

"What the--" Doggett exclaimed before the four of them jerked their heads towards the sudden movement that came from beside them.

"Don't worry, I just knocked them out for a few hours with the same stuff they gave us," Jackson said as he appeared beside them, producing a syringe. 

Scully breathed a sigh of relief before switching into doctor mode. "Well, we need to put a stop to the Spartan Virus and if these visions are correct, I will need to synthesize alien DNA in order to develop a viable vaccine." She turned to Mulder and Doggett, both whom were visibly ill and barely standing. 

"What is this Spartan Virus?" Doggett asked incredulously.

Monica sighed. "All of us were given Smallpox vaccinations as children, in these vaccinations we were introduced to a virus that would later strip us of Adenosine Deaminase, leading to the decimation of our immune systems. Dana and I, as well as Jackson, are the only ones who are not affected by the virus because alien DNA has the ability to decode the virus."

"You can't be serious. You're saying the government was privy to this, a vaccine that is given to everyone as a child for the purpose of later activating a virus?" John asked as he sank into a nearby chair.

"I bet Tad O'Malley is having a field day," Mulder said dryly.

Monica nodded. "Yes and all he had to do was activate it and it can happen overnight, within hours as it did."

"But he needed me to do it," Jackson supplied.

"Unless he found another way before he captured you and your mom."

Scully shook her head, frustrated. "Jackson...Monica, I'll need your help. I may not be able to get a large enough sample from myself without putting the baby at risk."

Monica nodded. "Of course."

"Yes, I'm in. Let's put an end to this," Jackson said. "We have a few hours before anyone here comes to."

Scully nodded. "Okay, but first Mulder and Doggett need fluids. Both of you need an IV right now before we do anything."

It didn't take long for Scully to find the supplies she needed before she had both the men laying down on exam tables with the administered IV. 

The next task was to draw an ample amount of blood from Monica and from Jackson before performing the PCR to synthesize the alien DNA component before extracting the cells needed to develop the vaccine.

Monica and Jackson sat patiently side by side as Scully donned the latex and got to work. 

"You were working with him," Jackson said simply. 

Monica turned to him and nodded. "I helped deliver you when your mom gave birth. You had been sought after since before you were born. Working with the smoking man afforded me access to information and allowed me credentials to ensure these men couldn't get to you. I appeared to give my services to him in exchange for access to the alien technology that would keep me safe upon hearing about his plans for this virus years ago. But really, my intent was to gain access to this information so I could ensure he couldn't get to you and allow your mom to be free from charges as a result of helping your dad escape the death penalty. Freeing your dad from those charges however wasn't so simple, but we dropped a lead on a case to the FBI back in 2008 and while knowing it would lead to Mulder resurfacing, we never predicted it would eventually lead to the reopening of the X-Files. Well,  _ he _ didn't anyway."

"You were the reason we no longer had to hide?" Scully asked. "That bastard gave himself all the credit."

Monica shrugged. "We knew your whereabouts the entire time. He lost interest for a while as he focused on his ultimate plan. Mulder being out of the way so to speak allowed him to orchestrate everything. I'm sorry I couldn't tell you sooner, Dana. I couldn't. Not at the risk of being discovered... if either of you sought any information it would have easily drawn suspicion. As long as all of you were safe for the time being, that's what mattered."

Scully teared up slightly. She closed her eyes and swallowed tightly. "You had come to me in a vision and told me all of this. You knew that we could stop it."

Monica managed a small smile. "That's right."

Scully stole a glance across the room at Mulder and Doggett, both who were resting. The IV fluids would only last so long. 

"As much as I want to express my gratitude, it's going to have to wait. I found something, Monica."

Monica frowned. "What is it, Dana?"

Scully looked between her and Jackson. Monica stood and walked over to where Scully was working under a microscope, working on the extraction needed to develop the vaccine.

Once they were out of earshot, Scully reached out to grasp Monica's forearms. 

"Monica, there was something else I found when analyzing your blood sample."

"What?" she pressed.

"There were ample levels of the hCG hormone in your blood. Now there are several things that can cause elevated levels of hCG, but pregnancy is the most common condition associated with it. And considering everything you've told me about what that smoking bastard has been up to..."

"You're saying I'm pregnant?"

Scully released a slow breath and nodded. "Cancer can also cause elevated levels of hCG, but considering the chip both of us have and our DNA, it would be unlikely.  We'd need to do an ultrasound to be sure just to rule out anything else, but I'm almost certain."

Monica's jaw fell open. "But..that's impossible..."

Scully couldn't help but laugh at the absurdity of it all. "That's what I said, but here we are."

"Wow. I mean, I know it can happen, but from my understanding, it takes  some outside assistance for women in their late forties to early fifties."

"As you said, Monica, the smoking man was doing experiments to lengthen a woman's childbearing years for whatever sick project he had in mind. I don't doubt that he involved you in some way."

"But...he hasn't been near me Dana, not in several months."

"Which is why we need to determine how far along you are. I have resources at Our Lady of Sorrows, I can help you get the tests you need to ensure the baby is okay."

Monica, baffled, nodded. 

"Congratulations by the way. I don't believe it's reaching to assume John is the father?"

Monica shrugged. "I can't tell you how long it's been since I've had a life in that aspect."

"He'll be thrilled I'm sure," Scully assured her. "But we'll get that testing done as soon as we're able."


	33. Chapter 33

It didn't take long for Scully to create a viable vaccine and she did not need Jackson's stem cells as originally anticipated. He hadn't been as bad off as he had in her vision when he was practically at death's door.

As Mulder and Doggett were recovering, Scully was amplifying the vaccine with the help of Monica.

Jackson had decided to take a look around the building, digging through files and any information he could find on Project Crossroads. He managed to snag a laptop before moving on and stopping in front of a door labeled "Initiation Room". 

The door was key padded as well and he closed his eyes for a moment, deep in concentration before the door clicked. He pushed it open. In this room was an array of computers. He was shocked no one was manning this area. Then again, he was sure he managed to disarm everyone in this building. 

He stopped in front of a computer with digital code scrolling upwards on the screen. As he touched the mouse it required a code to initialize. After several attempts of putting his hacking skills to work, he managed to break into the system - much as he had with Project Crossroads. He almost regretted poking his head around before as it led to being targeted by the DoD and the eventual death of his adoptive parents. Now, he really didn't have much to lose.

As time ticked by, he grew painfully aware of the limited time he had and he could sense his birth mother looking for him. That was when he realized this computer room wasn't just encrypted information being kept secret by the government, but they were part of a vessel, keeping someone or something alive.

And then the realization hit him.

\----

Upon finishing the vaccine, Scully had begun to panic once she noticed Jackson been gone for almost two hours. They had to get out of there.

A newly rejuvenated Mulder had raced outside to look for their son, fearing the worst, though Scully could sense he was fine. She was desperate to get them all out of there undetected before anyone came to.

Doggett helped gather everything they needed as Monica had ordered a chopper. When they refused, she said they had a vaccine for the virus which needed to be delivered to the hospital immediately.

She was thankful that they could get someone out here and those fallen infrastructures hadn't severed her ability to make contact. The last she had checked, gas stations had been overrun in the widespread panic and she wasn't sure any of them had enough gas to make it back.

"They'll be here in fifteen minutes," she said.

"I'm not leaving without him!" Scully cried.

"Dana, whatever these people were injected with, they'll come to any minute. We have to go if we're going to make it out of here alive."

"I'm here!"

Scully whirled around and let out a breath she hadn't realized she had been holding at the sight of her son.

"Oh, thank God!"

"I found the information I needed...information we all needed," he said indicating the laptop in his jacket.

"There is something else though. The Smoking Man, he's being kept alive by a regenerative system. A machine. The vessel is his life source. It's tied to some type of implant that allows him to regenerate. "

The four of them shared several confused glances. 

"Did you know anything about this, Monica?" Scully asked.

Monica shook her head. "I know he had access to technology that allowed him to make a remarkable discovery, but there were things he kept me in the dark about."

"It's why he's after me," Jackson continued. "With my DNA specifically, he wouldn't have the need for this computerized technology that keeps him alive. While his body theoretically has died several times, the implant remains, allowing him to regenerate over a period of time...all the while MY DNA would allow him to never have to rely on the chip or a server to keep him alive."

Mulder thought for a moment before turning to Scully. "The simulation, Scully. What if Spender had uploaded his consciousness at some point in time? Before we saw him in New Mexico? How else can you explain a man that should have died in that bombing, but didn't?"

Scully shook her head. "Erika Price and Mr. Y...Purlieu services were working against Spender, not with him, Mulder. You said it yourself."

"I know, but you saw what happened to Langley, Scully.  I think Spender consented to the simulation, but perhaps at some point when the two organizations separated, Spender was able to use the technology to upload his consciousness to a chip that has the ability to regenerate so he can never die. Why else would they want him dead as well?"

Scully sighed as she recalled shutting down the server at Titanpointe, but in the end, the system had been removed leaving no trace of it behind. The only proof it ever existed.

Jackson held up a small piece of metal between his fingers. "I found this...when I blew him up. We need to destroy it along with that server. It's the only way he'll stay dead."

"Why need a simulation if you have access to technology that allows you to live forever. Just when you think you know everything about a person," Monica quipped. 

Jackson turned to Scully. "Wouldn't that mean the vaccine you created with my DNA would allow people to live forever?"

Scully shook her head. "While I analyzed your DNA, it became apparent that all your alien DNA is active. That's why you have powers and abilities that myself and Monica do not. I only synthesized what was needed to disarm the virus."

Jackson started to nod but was suddenly startled by movement from the corner of the room. "We have to go, now. We have to destroy the vessel in that room and the rest of this place to end all of this."

Turning to Mulder, he said, "in exactly two minutes, I want you to set off the alarm in this place. The rest of you need to get out of here, now!"

Scully opened her mouth to respond, but her son had bolted from the room.  "William!"

"We have to hurry!" Doggett said, pointing to a man in a lab coat that was coming to. 

Scully raced to grab what she needed and before Mulder was about to run out the door, she grabbed onto his hand. "Don't leave without him...we can't leave without him."

"I will get him, you guys go."

"They're almost here," Monica said, disconnecting her phone.

"Hey, who are all of you?!" The man in the corner of the room demanded.


	34. Chapter 34

**Notes for the Chapter:**

> We're almost at the end...hope you all have enjoyed it so far. :)

Back in the initiation room, Jackson entered two passwords, Titanpointe and Blarney. He didn't expect the familiar booming robotic voice that came next.  "Well, you figured it out haven't you, Grandson. I certainly underestimated you. But, you are the son of Fox Mulder and Dana Scully."

"It's over asshole. I'm done running from you."

"This isn't the end," the voice blared. "I always find a way to come back."

Jackson stood up from the desk and raise his arms. "Not this time."

Closing his eyes, Jackson willed himself to concentrate completely on the task at hand. A moment later, he could hear the clamor of the alarm sounding throughout the building and he pushed the sound from his thought process as he felt heat radiate throughout his palm to his fingertips.

He yelled out pushing the surge of energy forward, sending sparks flying throughout the room and moments later, the room was lit in a blaze of electrical fire. With one last glance at the chip between his fingers, he hurled it toward the fire.

The computerized voice slurring as the electrical devices burned to the ground. The thrill overwhelmed his senses and he was unable to move as his feet. It felt as if they were cemented to the ground.

A loud rapping on the door broke his catatonic-like state. "Jackson!! Jackson, GET OUT OF THERE!"

The smoke drifted into his nostrils and he felt his knees weaken. A moment later, he was vaguely aware of distinctive coughing and movement beside him before he felt himself being pulled to his feet.

"I got you."

Mulder. 

"How did you get inside?" he mumbled, feeling strong hands wrapping around him. 

"Titanpointe...that was the password."

\-----

Our Lady of Sorrows Hospital

The hospital was a whirlwind of confusion and mass panic upon their arrival that had been expedited by the helicopter transport. Scully was now dressed her white lab coat, in complete doctor mode as she delegated orders and commands to the other hospital staff. Mulder found it sexy despite the circumstances. There were no words for what Scully's discovery would ultimately do for the medical world and the impact it would have on her career. As the vaccine had been replicated, Washington Memorial was the second hospital in receipt of the cure. Slowly, but surely, the widespread panic was slowing to a standstill.

Upon their arrival, they had wanted to examine Scully, who of course insisted she was fine, but Mulder had pleaded with her to ensure both she and their baby were fine. Once everything had checked out, they moved on to Jackson to check for carbon monoxide poisoning as he had taken in quite a bit of smoke before Mulder had gotten to him. He too was cleared as he appeared to be making a remarkable recovery. 

Monica and John went with Jackson to the cafeteria while Mulder perused the halls looking for Scully. The front desk was still overwhelmed with patients that he hadn't bothered to ask someone to page for her. She had had her share of work cut out for her and had been quite scarce the past few hours. He was growing worried about Scully overdoing it, putting herself on the back burner as she had done in the past. She had been up for over twenty-four hours and he was worried what the lack of sleep and having been on her feet for so long would do to her and the baby.

Finally, he saw her emerge from the elevator across the hall, engrossed in some paperwork that he assumed was a medical file. Her hair was now just long enough for her to pull back into a loose ponytail.

"Scully?"She continued flipping through the pages until he gently reached out for her arm, startling her. "Dana."

"Oh God, Mulder...I was just going to check on Skinner. He was admitted here last night and I made sure he was one of the first to receive the vaccine. He was in terrible shape."

Mulder nodded as he stared back at her, assessing her features for signs of stress and fatigue.  Sure enough, he could see lines of weariness that had settled there. "Scully...I think you've done everything you can. You need to rest, I know I don't need to say this but it isn't just about you."

Scully shook her head in annoyance. "You don't think I know that already?" she almost snapped. 

And there it was, frustrated and hormonal pregnant Scully. He wouldn't dare mention that though if he valued his life.

"I'm just saying, you deserve a break after everything that's happened."

Scully let out a long sigh, softening her tone. "I know...I just, I need to check on Skinner first, okay?"

Mulder nodded, placing a hand on her lower back as he followed her to Skinner's room. He too felt a sense of responsibility towards Skinner after all he had done for them.

As they stopped in the doorway, Mulder could see Skinner who was awake and sitting upright with an IV drip attached to his arm. He turned towards the doorway upon hearing them enter.

"Scully...Mulder, talk about a sight for sore eyes."

Scully looked up from the medical chart she was holding. "Sir...Walter, how are you feeling?"

Skinner managed a chuckle as he glanced at her belly. "Good, could be better I suppose, but good all things considered. I'm no longer knocking on death's door, so that's something. I mean it wouldn't be the first time. Dana, you not only found but engineered the cure. I have you to thank for that," he nodded towards Scully.

Scully smiled, reaching to gently touch his arm. "It looks like your immune system is almost entirely back to normal. You'll likely be released within the next few hours since we're still over capacity."

He nodded and turned towards Mulder who had been regarding Scully carefully. "You found him, didn't you? The Smoking Man?" he whispered.

Mulder nodded. "It's a long and complicated story. William killed him...he found his life source and destroyed it."

Skinner's brow furrowed as he opened his mouth. "The man survived a bombing in New Mexico..."

Scully and Mulder exchanged a glance, stealing a look towards the doorway to ensure no one overhead before Mulder continued. "It has to do with Purlieu services...why they were after him. In essence, Carl Gerhard Busch died back in 2002, but he had uploaded his consciousness to a simulation. He used alien technology to generate a host, but even that had its frailties. He needed William to be granted permanent immortality, but somehow he found a way to release the virus just before he captured him."

Skinner swallowed as he took in this information. "Is he okay? William?"

Scully teared up at the thought. Her son didn't have to keep running. "Yeah, he's with John and Monica downstairs."

"Good. I'm glad to hear it. You should rest now too, Dana. You've done far more than enough by creating a global cure to the Spartan virus. This is going to change your career in ways you never imagined possible.  Seeing what you both have accomplished, no matter all the pain and suffering you both have endured all these years...makes all those years of fighting for that basement office worth it, even if it meant losing a seat in the director's chair. I'd do it all over again."

She wasn't sure if it was the hormones or the aftermath of everything that's just happened catching up to her, but Scully felt her eyes start to well up with tears. "Thank you...Sir, Walter."

Mulder placed his hand gently on the small of Scully's back. "I'm sorry we ever doubted you, Sir.  I know you were trying to protect Scully and I. I meant what I said before, we're with you. Always."

A sudden movement at the door startled the three of them. It was Nurse Sandeep. "Doctor Scully? We need you."

Mulder regarded her carefully, communicating in that silent language of theirs. Scully sighed, not bothering to look back. "Page Doctor Tran, Sandeep. I believe my shift is over."


	35. Chapter 35

It had taken several weeks for the cure to reach a global level. There were only six thousand fatalities reported globally, which was quite low considering every populous was affected. However, the deaths reported were generally in third world nations in which immune systems were more easily compromised.

Scully's life-saving vaccine was trending all over the media and for a time, news reporters and other mass media outlets followed her everywhere. It was a mass phenomenon. Not only would Scully receive a substantial promotion, but her discovery meant they would never have to worry about finances again, not that they really had to anyways with both their inheritances. But Scully could face early retirement if she chose.

Another thing they had not expected was the large influx of gifts, mostly for Scully and the baby. Once the word had gotten out that she was pregnant, people from all over the world had sent her everything she could possibly need for the baby, from hand knit booties to breast pumps along with notes that included well wishes for her and the baby.

Most of these were young women who felt Scully had inspired them to pursue careers in medicine or science. Others were Mothers dealing with fertility expressing how she was an inspiration and living proof that miracles do happen. And it was true, the baby was a true miracle. 

Despite what Spender said about the implant, it did not explain how nothing resulted after all the years they spent together after William until now.

Though they were overwhelmed with gifts, Monica insisted on putting on the baby shower. She and John were now happily expecting as much as she was initially unsure how John would take being a father so late in life. It was welcome news to Mulder, who realized he would no longer be alone on the midlife fatherhood train. Scully was happy for their daughter to have another child her age to have play dates with as all her siblings had much older children and she didn't have many girlfriends.

“I never thought I’d say this Mulder, but I’m glad you re-installed that front gate,” Scully sighed from the couch, her hand rubbing gentle circles over her distended abdomen. With her face being all over the media, she was glad they were afforded with the extra privacy. 

Everything hurt these days and as much as she wanted to evict the cohabitor, she relished the remaining days she had with her daughter nestled safely beneath her heart, savoring every kick and hiccup that came from within. A true miracle, one that wasn't likely to repeat itself.

She was just weeks away from her due date and warm summer air settled into cool autumn nights. The fluorescent leaves of the trees outside started piling up around their property as they went ignored for far too long.

“You're a renown doctor, Scully. A prestigious icon. People will come from all over the world seeking your medical care should you choose to return,” Mulder beamed with pride. “Now if you'll excuse me for a few minutes, Jackson and I have a ball to catch and leaves to rake before I have to go and pick up your brother and his family from the airport. Holler if you need anything,” he said before disappearing out the door. 

Scully couldn't help but grin as Monica busied herself throughout the house. Her own bump was making itself known into her second trimester. Not long after the viral outbreak, Scully helped her friend seek the genetic testing she needed by a colleague she trusted implicitly. Everything checked out. She and Doggett were having a healthy baby.

“As much as I don't like surprises, you've really outdone yourself, Monica. Thank you.”

“You deserve this, Dana,” she smiled as she prepped the dining table and finished up final touches of the pink decorations in the house.

“I wouldn't have been able to develop that vaccine without you, Monica. You had come to me in my vision, knowing I'd develop the cure. You chose that particular moment to come to me even if the events didn't quite play out the same in the dream.”

Monica hesitated for a moment. Years of isolation had taken its toll on her, changed her in ways she never dreamed possible. But in the end, her efforts had been successful.

“I thought when Mulder shot him it would be over. I hoped that you and Mulder getting to William first would throw a wrench in his plans,” Monica said.

“And you risked your life to do so. I can't thank you enough. So...are you going to tell me what you're having? Have you found out yet?”

Monica narrowed her eyes as she regarded her friend from the kitchen. “Today is about you, Dana.”

“Everything has been about me lately. You deserve this. So tell me what you're having.”

“A girl,” Monica blurted out excitedly. 

“Oh Monica, that's great! I'm so happy for you!” She said as she tried to maneuver herself from the couch.

Monica rushed around to her friend. “No don't you dare get up,” she said as she leaned in for a hug, their bellies touching in typical pregnant best friends manner.

“And John?” Scully pressed.

“He's thrilled. We're going to call her Graciela after my mom. Gracie for short.”

“Beautiful name. It's just so nice not to be in this alone,” Scully admitted.

Monica nodded. “I'll admit, I never really thought about having kids or being a mom. I guess life really is like a box of chocolates, you never know what you're going to get.” she chuckled.

“I didn't either...think about being a Mom, that is. I was so focused on my career in medicine and later the FBI that I didn't really imagine the typical white picket fence until that choice was taken from me. Now look at us,” she laughed. “Pregnant in our fifties.”

They had almost forgotten about the men outside. Mulder, Jackson, and Doggett had been playing catch outside amidst Mulder's raking duties. Skinner and Kim were on their way over. Scully couldn't help but smirk at the thought...the irony of it, their boss with his assistant, but she couldn't be happier for him. He deserved it. They all did.

After opening their home to their wayward son, he meekly accepted their offer and moved in a few weeks back. It was tough with the press around. Technically Jackson was supposed to be dead. No doubt if anyone saw him it would raise suspicion. 

Money afforded them the ability to provide their son with a new identity. A fresh start. He and decided on William Douglas Jackson as his full name. It would be a few more weeks until it was all set in stone.

A little over an hour later, Mulder and Jackson had returned with Bill, Tara, and Matthew while Skinner and Kim had arrived shortly before.

It hadn't been easy breaking the news of her pregnancy to her brother, he still hated Mulder, but when she revealed they were legally married now and living together, it was one less strike against him.

Everyone helped themselves to finger foods as the coffee table filled with more gifts. Jackson and Matthew chatted. After they had gotten acquainted with one another, they found common ground with majors, bands and video games. Seeing her son interact with someone closer to his own age was such a relief and hearing him discuss the prospect of going back to school was even more so.

John passed through the dining area every so often to check up on Monica who had recently started having morning sickness again but was generally fine throughout the day. He spent some time catching up with Skinner as well, asking when the big day was.

Mulder admitted to the car ride being an awkward one, but Bill had been thrilled to finally meet William after all these years.

Once all the presents had been opened, Scully stole a trip to the bathroom and came out to see Bill in the hallway. “Dana, you got a minute?”

Scully nodded, smoothing a hand over her belly. “Sure, what is it, Bill?” she asked making sure everyone was out of earshot.

Bill was always very difficult to read despite growing up with him. His strict jawline indicated he always meant business.

“As you know, I don't like Mulder and I never will,” he said as Scully stiffened in irritation. “But I can see how happy you are and I hope to God it won't be taken away this time.”

Scully nodded. “It won't, Bill.”

“Good. I will take him to the desert myself if he hurts you again. Anyways, William...Jackson...seems like a good kid,” Bill continued as he sipped the mocktail in his hand, glancing over at Jackson and Matthew. “Mom always talked about him. I know she didn't want to show you how much the adoption affected her.”

It was like a knife to the heart. “Bill, if there was any other choice…”

He held out a hand to stop her. “I never understood it myself - your being blessed with a miracle and having to give it up, but Mom came around..”

Scully looked down, fiddling with the fabric of her maternity shirt as she waited for him to finish.

He swallowed. “I still don't quite understand everything that's happened with all of you. But Dana, the truth is..they'd both be so proud of you. I mean, look at what YOU have accomplished. You developed a life-saving cure. Dad would especially be proud.”

Scully felt tears well in her eyes as she rested against the wall. 

“And Mom,” he continued. “she always wanted a Granddaughter, but we couldn't give her one. She would spoil her rotten if she was here you know that?”

Scully placed a hand on her belly. “Yeah, she would have,” she agreed. “Thank you.”

“Dana, there you are,” Monica said as she approached them both in the hallway. “We can't start without the guest of honor...it's time for games and presents.”

Scully and Bill exchanged a look before Dana turned towards her. “I'll be right there, Monica. I just need a minute.”

As Monica disappeared from view, Scully saw Bill smile for the first time in ages. “You know, if I didn't know any better, I'd say she reminds me of--”

“Melissa,” Scully supplied with a smile.

Bill laughed. “She cornered me for fifteen minutes earlier telling me about my negative energy and how it wasn't good for you or the baby.”

“That's Monica. You should hear her do whale songs.”


	36. Chapter 36

**Notes for the Chapter:**

> This is it, everyone! I started this story on Instagram back in May and it made its way onto AO3. It'll be 2019 in just a few days. I started this story to bring some resolution to MSIV and M&S's story. Please let me know your thoughts in the comments and I hope you enjoy this as much as I did!

Katherine Lily Scully-Mulder made her grand debut into the world at 9:05 pm on October 13th after four hours of labor. Her little fists were balled up in displeasure at her entrance to the world if her clamorous cries were any indication.

It was a beautiful, welcome sound.

“You have a girl, congratulations!” 

Scully's own cries of happiness soon joined her daughter's as she was delivered onto her chest.

The baby needed skin to skin contact to help regulate body temperature as well as facilitate the bonding process. It was one of many things Mulder had learned in the several dozens of pregnancy, birth and parenting books he managed to read to occupy his time over the past few months.

Tears began to trek their way down his cheeks as he watched the baby quiet as Scully murmured words of love to her.

They both watched the baby, mesmerized and awestruck, completely oblivious to the nurses who toweled the baby down in order to clean her up a bit. The tears continued to come.

Dr. Andrews had asked Mulder to cut the cord and he happily obliged.

Scully sniffled as she gently stroked the soft tuft of brown hair on her daughter's head. “Happy Birthday to you...and to Daddy,” she whispered with a teary glance towards Mulder.

“Best birthday yet, Scully.”

They silence for a few moments, taking in every single feature. While her eyes remained closed, she had a little button nose and rosebud mouth that he was sure was Scully's. Along with the rich brown tufts of hair, her skin was slightly darker in coloring than he remembered William to be as an infant. The Mulder genes were making themselves known.

“Oh God, Mulder. She's so beautiful.”

“She takes after her mother that way.”

Minutes later, Dr. Andrews started to reach for the baby. “It's time for this little one's exam,” she said with a smile.

Scully instinctively clutched the baby closer to her chest and Kit began to whimper at the sudden movement. “No.”

Taken aback, she smiled softly. “She'll be back here in no time. It's just routine testing as you know...we need to get her Apgar score and clean her up.”

Mulder stood and placed a gentle hand on Scully's shoulder and she relaxed with a sigh. She was exhausted from labor and still needed to deliver the placenta.

Reluctantly, Scully relinquished the baby and then looked pointedly at Mulder. “You go with her,” she all but demanded. 

She reached for his arm as she looked at him with pleading eyes and he nodded, but not before leaning forward to place a soft kiss on her forehead. 

“We'll be right back,” Dr. Andrews promised with a smile. “Jen, if you could work on palpitating Dr. Scully's abdomen.”

The petite Filipino woman nodded. “Yes, doctor,” she said before moving to tend to Scully.

“Let's get you taken care of so you can spend time with your little one once she's done.”

Mulder watched his tiny baby daughter as she fussed, wriggling her little arms and legs in protest. The fact that this tiny person had been snatched from her mother's warmth so quickly infuriated him as his daughter wailed in protest at the separation. He couldn't be illogical about this, he told himself. These people were just doing their jobs. He sighed as he watched his daughter as she got weighed and had her measurements taken.

“This little lady has a perfect Apgar Score, a nine. Congratulations, Dad,” Dr. Andrews smiled.

Mulder swallowed the lump that had formed in his throat he hadn't realized was there. Once the baby was cleaned up, she had been wrapped in a blanket and was placed into Mulder's waiting arms.

“Hey there my little angel,” he whispered as he looked down at her. “It's okay, none of that.” As if on demand, the baby's eyes opened and she quieted almost instantly as she peered up at him. His heart lurched at the familiar blue eyes. With his left arm braced protectively around the baby, he moved to touch the tiny hands, nudging them open.

The baby flexed her tiny hand in order to grip onto Mulder's finger.

He had forgotten the doctor was there until she had broken the silence. “We need to bring her back to Mom so she can feed her.”

Once the after birth had been delivered and she had been cleaned up, Scully had dozed for a few minutes until she heard footsteps in the room.

She turned and gasped, drinking in the sight in front of her.

Kit had settled against her father’s shoulder while Mulder was grinning ear to ear. Scully had only witnessed such a smile on one other occasion just over seventeen years ago. 

“How is she?” Scully asked, her eyes pleading. “Is she okay?”

Mulder smiled as he looked from his baby daughter to the love of his life. “She's perfect Scully, absolutely perfect and healthy.”

“Let me see her,” she insisted, pushing herself into a seated position.

The baby let out a mewl in Mulder’s arms as he brought her closer to her mother. The nurse followed closely behind him as he moved to settle Kit on Scully’s chest.

Kit bobbed her head while licking her lips and Scully shifted the baby in her arms as she opened her hospital gown. 

Mulder watched in awe as Scully gently ran her finger over the baby's cheek, nudging her mouth open before the baby quickly latched on. 

Scully gasped at the contact briefly before settling with a contented sigh as the baby nursed. Looking down at the miracle in front of her, she smiled warmly as she ran her free hand through the thin brown strands of hair. 

“We can take her to the nursery in a little later while you rest or--”

“She's staying with us,” Scully interjected. 

The nurse was startled by Scully's abrupt tone before she smiled softly. 

“Great. Well as you know already, newborns adjust easier rooming in with their parents. I'll get everything ready for her.”

Mulder nodded in thanks as she left the room and Mulder moved next to Scully. They sat for several moments watching the little miracle they had created who was still suckling contentedly.

“For a moment, when I woke up and you both weren't here, I thought it was all a dream. I still can't believe she's here,” Scully's voice broke, her eyes never leaving the infant in front of her.

“Against all odds,” Mulder murmured as he reached over to push back a wet piece of hair that stuck to Scully's face.

Scully laughed as she allowed the tears to fall.

“She has your eyes,” Mulder added. “And nose, Thank God.”

“Well Mulder, babies eye color can change over time. Just look at William. She definitely has your lips and coloring though,” Scully smiled.

As the baby unlatched from her breast, Scully placed a gentle kiss on her forehead.  “We love you baby girl.”

All three of them were given matching medical ID bands and not long after, the birth certificate had been signed, marking Katherine Lily Scully-Mulder's entrance into the world.

In the following hours, upon hearing the news, Monica, John, and Skinner had dropped by to meet the newest member of their family. Once Scully had been moved to her own room, she was showered with flowers and cards. The birth of Scully and Mulder's child became widespread news as expected.

Scully felt a pang in her heart. There was only one person missing that kept them from feeling complete. 

Scully smiled at her daughter as she held her, perfectly swaddled in her blanket. “You have a big brother Katie girl. His name is William, but he goes by Jackson now. I hope you get to meet him soon.”

“I hope soon means right now,” said a voice from the doorway.

Scully gasped, turning towards the doorway to see Jackson carrying a bouquet mixed with white roses and lilies.

“Oh, Jackson, they're beautiful,” she said as her eyes welled with tears.

“Crystal suggested roses and lilies. Her middle name and Kate's middle name,” he said with a lopsided smile that reminded Scully all too much of Mulder.

Crystal, whose middle name was Rose, was Jackson's new girlfriend. They had only met her a handful of times, but they were already quite fond of her and most importantly, she brought light into Jackson's eyes they hadn't seen before. For the first time in years, he was happy. 

Jackson took in the scene before him, of his mother carrying his sister in her grip. He moved to find a spot for the flowers at her bedside table.

“I'm sorry I'm late.”

Scully opened her mouth to respond before Mulder appeared in the doorway with a bag of takeout. 

“Hey,” he said, placing his hand on Jackson's shoulder.

“Are you sure I'm not imposing?” He asked.

“No!” Both Scully and Mulder rushed to say at once.

Glancing at one another, Scully continued. “We're so glad you came.”

Jackson smiled. “I knew you would be okay and Kate too, but I wanted to see for myself.”

Once she realized she was no longer the center of attention, Katie began to whimper. Scully turned back towards the baby. “Shh, it's okay sweetheart.”

Jackson stared at his sister, mesmerized. “She's so little,” he admonished. 

“You were that small at one point too,” Mulder chuckled.

Scully glanced from the baby back to Jackson, debating on her next move. She didn't want to push her son but decided to extend the invitation anyways. She lifted the baby towards him. 

“Would you like to hold her?”

Jackson hesitated for a moment, looking between her and Mulder and then back at the tiny bundle in Dana's hands.

“Are you sure?”

Scully laughed. “Are we sure? You're our son. Her brother. Of course, you can hold her. I mean, only if you want to.”

Jackson licked his lips as he watched the baby turn her head as if sensing his presence, tiny arms extended out.

Closing the distance between them, he extended his arms and allowed his mother to place the baby into his arms as she explained to him how to hold her properly and support her head.

Once Katie was securely in his arms, he moved to sit in the chair beside Mulder. 

Mulder moved to sit beside Scully on the hospital bed, wrapping his arm around her as they watched both their children together.

Jackson watched the tiny bundle as she scrunched up her red face and he stiffened, bracing himself for a full-out wail. To his surprise, she let out a small yawn as she stretched her tiny limbs before settling into his arms, eyes wide and staring back at him, watching him intently.

“I hear you talking about who she looks more like,” he said pointedly at Mulder and Scully. “Newborns just look like potatoes to me. But she seems to have Dana's eyes and Mulder's hair.” That earned him a laugh from both. 

He looked down at the baby who was fascinated by this new person holding her. It was then that Jackson felt an overwhelming warmth, it was an unusual sensation and suddenly he felt perfectly at ease holding this tiny person as if they had already known one another for a lifetime.

“Hey Katie, I'm your big brother.”

END

**Notes for the Chapter:**

> I hope you enjoyed the birth of Katherine Lily Scully Mulder. :) There WILL be more, but since I wrapped up the mytharc, I decided it would be more fitting to start a new installment that explores how Mulder and Scully navigate parenthood. I hope you all enjoyed it! Thanks for sticking around and reading if you made it this far!!!


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